Multiple sequence alignment - TraesCS4B01G166100

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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 TraesCS4B01G166100 chr4B 100.000 2585 0 0 1 2585 357907838 357910422 0.000000e+00 4774.0
1 TraesCS4B01G166100 chr4A 89.481 2082 145 31 535 2585 261874327 261876365 0.000000e+00 2564.0
2 TraesCS4B01G166100 chr4A 86.787 333 23 4 13 327 261874003 261874332 4.090000e-93 351.0
3 TraesCS4B01G166100 chr4A 94.215 121 6 1 374 493 687422429 687422549 1.580000e-42 183.0
4 TraesCS4B01G166100 chr1D 88.949 1285 105 21 707 1966 34637824 34639096 0.000000e+00 1552.0
5 TraesCS4B01G166100 chr1D 88.235 323 26 7 1991 2303 34639192 34639512 2.430000e-100 375.0
6 TraesCS4B01G166100 chr1A 88.303 1308 113 22 711 1991 33020712 33022006 0.000000e+00 1531.0
7 TraesCS4B01G166100 chr1A 82.558 258 14 19 2194 2443 33022212 33022446 5.640000e-47 198.0
8 TraesCS4B01G166100 chr1B 89.354 1099 87 22 732 1804 53050797 53051891 0.000000e+00 1354.0
9 TraesCS4B01G166100 chr1B 87.368 285 23 8 2030 2303 53052253 53052535 5.370000e-82 315.0
10 TraesCS4B01G166100 chr1B 83.824 68 8 3 314 380 364070877 364070812 7.720000e-06 62.1
11 TraesCS4B01G166100 chr3B 96.610 118 3 1 376 492 692838250 692838367 7.300000e-46 195.0
12 TraesCS4B01G166100 chr3B 94.958 119 5 1 375 492 798492087 798492205 4.390000e-43 185.0
13 TraesCS4B01G166100 chr3B 96.226 53 2 0 327 379 714439016 714439068 1.270000e-13 87.9
14 TraesCS4B01G166100 chr3B 94.340 53 3 0 327 379 61531576 61531524 5.930000e-12 82.4
15 TraesCS4B01G166100 chr3B 93.878 49 2 1 489 536 823030392 823030344 3.570000e-09 73.1
16 TraesCS4B01G166100 chr3B 97.297 37 1 0 498 534 528610692 528610656 2.150000e-06 63.9
17 TraesCS4B01G166100 chr3B 96.970 33 1 0 322 354 423807373 423807405 3.590000e-04 56.5
18 TraesCS4B01G166100 chr7D 95.726 117 4 1 377 492 45626807 45626691 1.220000e-43 187.0
19 TraesCS4B01G166100 chr7D 94.340 53 3 0 326 378 57100325 57100377 5.930000e-12 82.4
20 TraesCS4B01G166100 chr5D 95.000 120 5 1 374 492 473359764 473359883 1.220000e-43 187.0
21 TraesCS4B01G166100 chr5D 95.726 117 4 1 377 492 561910279 561910163 1.220000e-43 187.0
22 TraesCS4B01G166100 chr5D 94.872 39 2 0 324 362 549552829 549552867 7.720000e-06 62.1
23 TraesCS4B01G166100 chr7B 92.913 127 7 2 368 493 462842241 462842116 1.580000e-42 183.0
24 TraesCS4B01G166100 chr7B 92.188 128 8 2 374 499 78550030 78550157 2.040000e-41 180.0
25 TraesCS4B01G166100 chr7B 96.296 54 2 0 326 379 161436232 161436179 3.540000e-14 89.8
26 TraesCS4B01G166100 chr5A 93.496 123 7 1 377 498 525710142 525710020 5.680000e-42 182.0
27 TraesCS4B01G166100 chr5A 92.982 57 3 1 489 545 135538187 135538132 5.930000e-12 82.4
28 TraesCS4B01G166100 chr5A 94.231 52 3 0 489 540 99555437 99555488 2.130000e-11 80.5
29 TraesCS4B01G166100 chr2D 90.909 66 6 0 314 379 441584779 441584844 3.540000e-14 89.8
30 TraesCS4B01G166100 chr2D 89.796 49 5 0 491 539 649610348 649610300 2.150000e-06 63.9
31 TraesCS4B01G166100 chr3A 96.154 52 2 0 328 379 34612588 34612639 4.580000e-13 86.1
32 TraesCS4B01G166100 chr6B 94.444 54 3 0 326 379 276668818 276668871 1.650000e-12 84.2
33 TraesCS4B01G166100 chr6B 84.375 64 6 4 319 380 412155575 412155514 2.780000e-05 60.2
34 TraesCS4B01G166100 chrUn 92.727 55 4 0 325 379 458430032 458429978 2.130000e-11 80.5
35 TraesCS4B01G166100 chr4D 94.231 52 3 0 489 540 238299937 238299886 2.130000e-11 80.5
36 TraesCS4B01G166100 chr6A 91.379 58 4 1 323 379 381087497 381087554 7.670000e-11 78.7
37 TraesCS4B01G166100 chr5B 84.091 88 7 7 327 409 565015797 565015882 7.670000e-11 78.7
38 TraesCS4B01G166100 chr7A 89.474 57 6 0 323 379 68089365 68089421 3.570000e-09 73.1
39 TraesCS4B01G166100 chr2A 90.385 52 5 0 319 370 615288748 615288799 4.620000e-08 69.4
40 TraesCS4B01G166100 chr2A 93.023 43 3 0 498 540 603991648 603991690 2.150000e-06 63.9
41 TraesCS4B01G166100 chr6D 85.294 68 7 3 314 380 355436589 355436654 1.660000e-07 67.6


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 TraesCS4B01G166100 chr4B 357907838 357910422 2584 False 4774.0 4774 100.0000 1 2585 1 chr4B.!!$F1 2584
1 TraesCS4B01G166100 chr4A 261874003 261876365 2362 False 1457.5 2564 88.1340 13 2585 2 chr4A.!!$F2 2572
2 TraesCS4B01G166100 chr1D 34637824 34639512 1688 False 963.5 1552 88.5920 707 2303 2 chr1D.!!$F1 1596
3 TraesCS4B01G166100 chr1A 33020712 33022446 1734 False 864.5 1531 85.4305 711 2443 2 chr1A.!!$F1 1732
4 TraesCS4B01G166100 chr1B 53050797 53052535 1738 False 834.5 1354 88.3610 732 2303 2 chr1B.!!$F1 1571

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
53 54 0.038526 TCTTGCTCGTTTCCTCCGTC 60.039 55.0 0.00 0.0 0.00 4.79 F
167 168 0.249489 ATGAGGTGATAACCGCTCGC 60.249 55.0 4.41 0.0 34.28 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1430 0.042188 CAAAGTCACCAACTGCGACG 60.042 55.0 0.00 0.00 38.58 5.12 R
1612 1676 0.947244 GAACAGGCATATGCTTCCCG 59.053 55.0 26.12 10.52 41.70 5.14 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.810755 CCCTCGTTGGCTTCCTTTTAC 59.189 52.381 0.00 0.00 0.00 2.01
35 36 1.613270 CTTTTACGCCCGCAACATTC 58.387 50.000 0.00 0.00 0.00 2.67
42 43 1.135315 CCCGCAACATTCTTGCTCG 59.865 57.895 3.72 0.00 42.87 5.03
53 54 0.038526 TCTTGCTCGTTTCCTCCGTC 60.039 55.000 0.00 0.00 0.00 4.79
63 64 2.443016 CCTCCGTCTCCCCTCCTG 60.443 72.222 0.00 0.00 0.00 3.86
82 83 2.963371 AGTCGCGACTCTGAACCC 59.037 61.111 34.98 7.77 36.92 4.11
88 89 1.360820 GCGACTCTGAACCCTAAAGC 58.639 55.000 0.00 0.00 0.00 3.51
121 122 0.654683 CAGCAGGAGCAATAACTCGC 59.345 55.000 0.00 0.00 45.49 5.03
126 127 0.868602 GGAGCAATAACTCGCGCGTA 60.869 55.000 30.98 15.77 37.57 4.42
152 153 7.023575 CGAAATTTCCTCCAGTAAAACATGAG 58.976 38.462 12.54 0.00 0.00 2.90
153 154 6.840780 AATTTCCTCCAGTAAAACATGAGG 57.159 37.500 0.00 0.00 38.64 3.86
167 168 0.249489 ATGAGGTGATAACCGCTCGC 60.249 55.000 4.41 0.00 34.28 5.03
177 178 2.354072 CCGCTCGCGATCCTTCTC 60.354 66.667 10.36 0.00 42.83 2.87
182 183 2.103143 CGCGATCCTTCTCTGCGT 59.897 61.111 0.00 0.00 43.50 5.24
217 218 6.260271 TCTCATTCTTGATCAGATTCATGTGC 59.740 38.462 0.00 0.00 0.00 4.57
260 279 1.959282 GCTGGGATGGGATTGATTGAC 59.041 52.381 0.00 0.00 0.00 3.18
321 340 7.910584 TCTGCATATGGTCTTGTATGTCATAT 58.089 34.615 4.56 0.00 33.01 1.78
322 341 9.034800 TCTGCATATGGTCTTGTATGTCATATA 57.965 33.333 4.56 0.00 31.99 0.86
323 342 9.310716 CTGCATATGGTCTTGTATGTCATATAG 57.689 37.037 4.56 0.00 31.99 1.31
324 343 8.815912 TGCATATGGTCTTGTATGTCATATAGT 58.184 33.333 4.56 0.00 31.99 2.12
336 355 9.682465 TGTATGTCATATAGTATGTACTCCCTC 57.318 37.037 0.00 0.00 37.73 4.30
337 356 9.122779 GTATGTCATATAGTATGTACTCCCTCC 57.877 40.741 0.00 0.00 37.73 4.30
338 357 7.098845 TGTCATATAGTATGTACTCCCTCCA 57.901 40.000 0.00 0.00 37.73 3.86
339 358 7.709601 TGTCATATAGTATGTACTCCCTCCAT 58.290 38.462 0.00 0.00 37.73 3.41
340 359 7.834681 TGTCATATAGTATGTACTCCCTCCATC 59.165 40.741 0.00 0.00 37.73 3.51
341 360 7.285858 GTCATATAGTATGTACTCCCTCCATCC 59.714 44.444 0.00 0.00 37.73 3.51
342 361 3.261818 AGTATGTACTCCCTCCATCCC 57.738 52.381 0.00 0.00 0.00 3.85
343 362 2.522705 AGTATGTACTCCCTCCATCCCA 59.477 50.000 0.00 0.00 0.00 4.37
344 363 2.587060 ATGTACTCCCTCCATCCCAA 57.413 50.000 0.00 0.00 0.00 4.12
345 364 2.352561 TGTACTCCCTCCATCCCAAA 57.647 50.000 0.00 0.00 0.00 3.28
346 365 2.638325 TGTACTCCCTCCATCCCAAAA 58.362 47.619 0.00 0.00 0.00 2.44
347 366 3.197983 TGTACTCCCTCCATCCCAAAAT 58.802 45.455 0.00 0.00 0.00 1.82
348 367 4.376223 TGTACTCCCTCCATCCCAAAATA 58.624 43.478 0.00 0.00 0.00 1.40
349 368 4.791334 TGTACTCCCTCCATCCCAAAATAA 59.209 41.667 0.00 0.00 0.00 1.40
350 369 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
351 370 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
352 371 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
353 372 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
354 373 4.045334 TCCCTCCATCCCAAAATAAGTGTT 59.955 41.667 0.00 0.00 0.00 3.32
355 374 4.777366 CCCTCCATCCCAAAATAAGTGTTT 59.223 41.667 0.00 0.00 0.00 2.83
356 375 5.105351 CCCTCCATCCCAAAATAAGTGTTTC 60.105 44.000 0.00 0.00 0.00 2.78
357 376 5.480073 CCTCCATCCCAAAATAAGTGTTTCA 59.520 40.000 0.00 0.00 0.00 2.69
358 377 6.014669 CCTCCATCCCAAAATAAGTGTTTCAA 60.015 38.462 0.00 0.00 0.00 2.69
359 378 6.754193 TCCATCCCAAAATAAGTGTTTCAAC 58.246 36.000 0.00 0.00 0.00 3.18
360 379 6.553100 TCCATCCCAAAATAAGTGTTTCAACT 59.447 34.615 0.00 0.00 0.00 3.16
361 380 7.070571 TCCATCCCAAAATAAGTGTTTCAACTT 59.929 33.333 0.00 0.00 42.89 2.66
362 381 7.714813 CCATCCCAAAATAAGTGTTTCAACTTT 59.285 33.333 0.00 0.00 40.77 2.66
363 382 8.550376 CATCCCAAAATAAGTGTTTCAACTTTG 58.450 33.333 0.00 0.00 40.77 2.77
364 383 6.536941 TCCCAAAATAAGTGTTTCAACTTTGC 59.463 34.615 0.00 0.00 40.77 3.68
365 384 6.314896 CCCAAAATAAGTGTTTCAACTTTGCA 59.685 34.615 0.00 0.00 40.77 4.08
366 385 7.179410 CCAAAATAAGTGTTTCAACTTTGCAC 58.821 34.615 0.00 0.00 40.77 4.57
367 386 7.064490 CCAAAATAAGTGTTTCAACTTTGCACT 59.936 33.333 0.00 0.00 40.77 4.40
368 387 9.081997 CAAAATAAGTGTTTCAACTTTGCACTA 57.918 29.630 0.00 0.00 40.77 2.74
369 388 9.646427 AAAATAAGTGTTTCAACTTTGCACTAA 57.354 25.926 0.00 0.00 40.77 2.24
370 389 8.628882 AATAAGTGTTTCAACTTTGCACTAAC 57.371 30.769 0.00 0.00 40.77 2.34
371 390 5.897377 AGTGTTTCAACTTTGCACTAACT 57.103 34.783 0.00 0.00 38.46 2.24
372 391 6.267496 AGTGTTTCAACTTTGCACTAACTT 57.733 33.333 0.00 0.00 38.46 2.66
373 392 6.687604 AGTGTTTCAACTTTGCACTAACTTT 58.312 32.000 0.00 0.00 38.46 2.66
374 393 7.822658 AGTGTTTCAACTTTGCACTAACTTTA 58.177 30.769 0.00 0.00 38.46 1.85
375 394 7.968405 AGTGTTTCAACTTTGCACTAACTTTAG 59.032 33.333 0.00 0.00 38.46 1.85
376 395 7.753580 GTGTTTCAACTTTGCACTAACTTTAGT 59.246 33.333 0.00 0.00 44.42 2.24
377 396 8.948145 TGTTTCAACTTTGCACTAACTTTAGTA 58.052 29.630 1.30 0.00 41.82 1.82
378 397 9.218359 GTTTCAACTTTGCACTAACTTTAGTAC 57.782 33.333 1.30 0.00 41.82 2.73
379 398 8.726870 TTCAACTTTGCACTAACTTTAGTACT 57.273 30.769 0.00 0.00 41.82 2.73
380 399 8.361592 TCAACTTTGCACTAACTTTAGTACTC 57.638 34.615 0.00 0.00 41.82 2.59
381 400 7.440255 TCAACTTTGCACTAACTTTAGTACTCC 59.560 37.037 0.00 0.00 41.82 3.85
382 401 6.228995 ACTTTGCACTAACTTTAGTACTCCC 58.771 40.000 0.00 0.00 41.82 4.30
383 402 6.042897 ACTTTGCACTAACTTTAGTACTCCCT 59.957 38.462 0.00 0.00 41.82 4.20
384 403 5.656213 TGCACTAACTTTAGTACTCCCTC 57.344 43.478 0.00 0.00 41.82 4.30
385 404 4.465305 TGCACTAACTTTAGTACTCCCTCC 59.535 45.833 0.00 0.00 41.82 4.30
386 405 4.710865 GCACTAACTTTAGTACTCCCTCCT 59.289 45.833 0.00 0.00 41.82 3.69
387 406 5.163530 GCACTAACTTTAGTACTCCCTCCTC 60.164 48.000 0.00 0.00 41.82 3.71
388 407 5.360429 CACTAACTTTAGTACTCCCTCCTCC 59.640 48.000 0.00 0.00 41.82 4.30
389 408 3.015675 ACTTTAGTACTCCCTCCTCCG 57.984 52.381 0.00 0.00 0.00 4.63
390 409 2.308690 CTTTAGTACTCCCTCCTCCGG 58.691 57.143 0.00 0.00 0.00 5.14
391 410 1.600058 TTAGTACTCCCTCCTCCGGA 58.400 55.000 2.93 2.93 0.00 5.14
392 411 1.600058 TAGTACTCCCTCCTCCGGAA 58.400 55.000 5.23 0.00 0.00 4.30
393 412 0.708802 AGTACTCCCTCCTCCGGAAA 59.291 55.000 5.23 0.00 0.00 3.13
394 413 1.291335 AGTACTCCCTCCTCCGGAAAT 59.709 52.381 5.23 0.00 0.00 2.17
395 414 2.517127 AGTACTCCCTCCTCCGGAAATA 59.483 50.000 5.23 0.00 0.00 1.40
396 415 1.790818 ACTCCCTCCTCCGGAAATAC 58.209 55.000 5.23 0.00 0.00 1.89
397 416 1.291335 ACTCCCTCCTCCGGAAATACT 59.709 52.381 5.23 0.00 0.00 2.12
398 417 2.292984 ACTCCCTCCTCCGGAAATACTT 60.293 50.000 5.23 0.00 0.00 2.24
399 418 2.103263 CTCCCTCCTCCGGAAATACTTG 59.897 54.545 5.23 0.00 0.00 3.16
400 419 1.838077 CCCTCCTCCGGAAATACTTGT 59.162 52.381 5.23 0.00 0.00 3.16
401 420 2.158943 CCCTCCTCCGGAAATACTTGTC 60.159 54.545 5.23 0.00 0.00 3.18
402 421 2.481449 CCTCCTCCGGAAATACTTGTCG 60.481 54.545 5.23 0.00 0.00 4.35
403 422 1.479323 TCCTCCGGAAATACTTGTCGG 59.521 52.381 5.23 0.00 41.80 4.79
404 423 1.479323 CCTCCGGAAATACTTGTCGGA 59.521 52.381 5.23 0.00 46.06 4.55
405 424 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
406 425 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
407 426 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
408 427 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
409 428 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
410 429 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
411 430 4.679639 CGGAAATACTTGTCGGAGGAATGA 60.680 45.833 0.00 0.00 0.00 2.57
412 431 5.183228 GGAAATACTTGTCGGAGGAATGAA 58.817 41.667 0.00 0.00 0.00 2.57
413 432 5.823045 GGAAATACTTGTCGGAGGAATGAAT 59.177 40.000 0.00 0.00 0.00 2.57
414 433 6.238484 GGAAATACTTGTCGGAGGAATGAATG 60.238 42.308 0.00 0.00 0.00 2.67
415 434 3.703001 ACTTGTCGGAGGAATGAATGT 57.297 42.857 0.00 0.00 0.00 2.71
416 435 4.819105 ACTTGTCGGAGGAATGAATGTA 57.181 40.909 0.00 0.00 0.00 2.29
417 436 5.359194 ACTTGTCGGAGGAATGAATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
418 437 5.360591 ACTTGTCGGAGGAATGAATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
419 438 5.129485 ACTTGTCGGAGGAATGAATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
420 439 6.323996 ACTTGTCGGAGGAATGAATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
421 440 6.332735 TGTCGGAGGAATGAATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
422 441 6.068670 TGTCGGAGGAATGAATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
423 442 6.016192 TGTCGGAGGAATGAATGTATCTAGAC 60.016 42.308 0.00 0.00 0.00 2.59
424 443 5.181433 TCGGAGGAATGAATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
425 444 5.048643 CGGAGGAATGAATGTATCTAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
426 445 6.148976 CGGAGGAATGAATGTATCTAGACGTA 59.851 42.308 0.00 0.00 0.00 3.57
427 446 7.148222 CGGAGGAATGAATGTATCTAGACGTAT 60.148 40.741 0.00 0.00 0.00 3.06
428 447 8.524487 GGAGGAATGAATGTATCTAGACGTATT 58.476 37.037 0.00 0.00 0.00 1.89
429 448 9.915629 GAGGAATGAATGTATCTAGACGTATTT 57.084 33.333 0.00 0.00 0.00 1.40
478 497 8.786826 ATGTATTTCTTCGACAAGTATTTCCA 57.213 30.769 0.00 0.00 0.00 3.53
479 498 8.251750 TGTATTTCTTCGACAAGTATTTCCAG 57.748 34.615 0.00 0.00 0.00 3.86
480 499 8.092068 TGTATTTCTTCGACAAGTATTTCCAGA 58.908 33.333 0.00 0.00 0.00 3.86
481 500 6.780706 TTTCTTCGACAAGTATTTCCAGAC 57.219 37.500 0.00 0.00 0.00 3.51
482 501 4.482386 TCTTCGACAAGTATTTCCAGACG 58.518 43.478 0.00 0.00 0.00 4.18
483 502 3.226346 TCGACAAGTATTTCCAGACGG 57.774 47.619 0.00 0.00 0.00 4.79
484 503 2.821378 TCGACAAGTATTTCCAGACGGA 59.179 45.455 0.00 0.00 40.60 4.69
485 504 3.119602 TCGACAAGTATTTCCAGACGGAG 60.120 47.826 0.00 0.00 44.10 4.63
486 505 3.522553 GACAAGTATTTCCAGACGGAGG 58.477 50.000 0.00 0.00 44.10 4.30
487 506 2.236395 ACAAGTATTTCCAGACGGAGGG 59.764 50.000 0.00 0.00 44.10 4.30
488 507 2.500098 CAAGTATTTCCAGACGGAGGGA 59.500 50.000 0.00 0.00 44.10 4.20
489 508 2.389715 AGTATTTCCAGACGGAGGGAG 58.610 52.381 0.00 0.00 44.10 4.30
490 509 2.108970 GTATTTCCAGACGGAGGGAGT 58.891 52.381 0.00 0.00 44.10 3.85
491 510 2.544844 ATTTCCAGACGGAGGGAGTA 57.455 50.000 0.00 0.00 44.10 2.59
492 511 1.553706 TTTCCAGACGGAGGGAGTAC 58.446 55.000 0.00 0.00 44.10 2.73
493 512 0.406750 TTCCAGACGGAGGGAGTACA 59.593 55.000 0.00 0.00 44.10 2.90
494 513 0.406750 TCCAGACGGAGGGAGTACAA 59.593 55.000 0.00 0.00 35.91 2.41
495 514 1.203087 TCCAGACGGAGGGAGTACAAA 60.203 52.381 0.00 0.00 35.91 2.83
496 515 1.204941 CCAGACGGAGGGAGTACAAAG 59.795 57.143 0.00 0.00 0.00 2.77
497 516 1.893801 CAGACGGAGGGAGTACAAAGT 59.106 52.381 0.00 0.00 0.00 2.66
498 517 2.299297 CAGACGGAGGGAGTACAAAGTT 59.701 50.000 0.00 0.00 0.00 2.66
499 518 2.299297 AGACGGAGGGAGTACAAAGTTG 59.701 50.000 0.00 0.00 0.00 3.16
500 519 2.036862 GACGGAGGGAGTACAAAGTTGT 59.963 50.000 1.75 1.75 44.86 3.32
501 520 3.233507 ACGGAGGGAGTACAAAGTTGTA 58.766 45.455 0.00 0.00 42.35 2.41
514 533 6.688637 ACAAAGTTGTACCAAGGTTAAGAC 57.311 37.500 0.00 0.00 40.16 3.01
515 534 6.181908 ACAAAGTTGTACCAAGGTTAAGACA 58.818 36.000 0.00 0.00 40.16 3.41
516 535 6.094464 ACAAAGTTGTACCAAGGTTAAGACAC 59.906 38.462 0.00 0.00 40.16 3.67
517 536 5.625568 AGTTGTACCAAGGTTAAGACACT 57.374 39.130 0.00 0.00 0.00 3.55
518 537 5.997843 AGTTGTACCAAGGTTAAGACACTT 58.002 37.500 0.00 0.00 0.00 3.16
519 538 7.128234 AGTTGTACCAAGGTTAAGACACTTA 57.872 36.000 0.00 0.00 0.00 2.24
520 539 7.742767 AGTTGTACCAAGGTTAAGACACTTAT 58.257 34.615 0.00 0.00 0.00 1.73
521 540 8.215736 AGTTGTACCAAGGTTAAGACACTTATT 58.784 33.333 0.00 0.00 0.00 1.40
522 541 8.843262 GTTGTACCAAGGTTAAGACACTTATTT 58.157 33.333 0.00 0.00 0.00 1.40
523 542 8.983702 TGTACCAAGGTTAAGACACTTATTTT 57.016 30.769 0.00 0.00 0.00 1.82
526 545 8.631480 ACCAAGGTTAAGACACTTATTTTAGG 57.369 34.615 0.00 0.00 0.00 2.69
527 546 8.442374 ACCAAGGTTAAGACACTTATTTTAGGA 58.558 33.333 0.00 0.00 0.00 2.94
528 547 8.727910 CCAAGGTTAAGACACTTATTTTAGGAC 58.272 37.037 0.00 0.00 0.00 3.85
529 548 8.440833 CAAGGTTAAGACACTTATTTTAGGACG 58.559 37.037 0.00 0.00 0.00 4.79
530 549 7.101700 AGGTTAAGACACTTATTTTAGGACGG 58.898 38.462 0.00 0.00 0.00 4.79
531 550 7.038799 AGGTTAAGACACTTATTTTAGGACGGA 60.039 37.037 0.00 0.00 0.00 4.69
532 551 7.277319 GGTTAAGACACTTATTTTAGGACGGAG 59.723 40.741 0.00 0.00 0.00 4.63
533 552 5.340439 AGACACTTATTTTAGGACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
574 593 1.420138 GTCTGGAAGTTGGGACTTGGA 59.580 52.381 0.00 0.00 45.88 3.53
575 594 1.699634 TCTGGAAGTTGGGACTTGGAG 59.300 52.381 0.00 0.00 45.88 3.86
576 595 1.421646 CTGGAAGTTGGGACTTGGAGT 59.578 52.381 0.00 0.00 45.88 3.85
577 596 1.420138 TGGAAGTTGGGACTTGGAGTC 59.580 52.381 0.00 0.00 45.88 3.36
578 597 1.700186 GGAAGTTGGGACTTGGAGTCT 59.300 52.381 7.90 0.00 45.88 3.24
579 598 2.551071 GGAAGTTGGGACTTGGAGTCTG 60.551 54.545 7.90 0.00 45.88 3.51
588 608 1.421268 ACTTGGAGTCTGGACATTGCA 59.579 47.619 3.51 0.00 0.00 4.08
601 621 4.517453 TGGACATTGCACCTTGTAAGTTAC 59.483 41.667 6.06 6.06 0.00 2.50
621 641 4.222124 ACTGTATTTCTTTCTCCCGCAT 57.778 40.909 0.00 0.00 0.00 4.73
622 642 4.589908 ACTGTATTTCTTTCTCCCGCATT 58.410 39.130 0.00 0.00 0.00 3.56
623 643 5.010282 ACTGTATTTCTTTCTCCCGCATTT 58.990 37.500 0.00 0.00 0.00 2.32
624 644 5.476945 ACTGTATTTCTTTCTCCCGCATTTT 59.523 36.000 0.00 0.00 0.00 1.82
657 681 5.677319 TCTTAGTTAGGCACAAGTATGCT 57.323 39.130 0.00 0.00 45.38 3.79
660 684 6.605995 TCTTAGTTAGGCACAAGTATGCTAGA 59.394 38.462 0.00 0.00 45.38 2.43
665 689 7.875041 AGTTAGGCACAAGTATGCTAGATATTG 59.125 37.037 0.00 0.00 45.38 1.90
670 694 6.454848 GCACAAGTATGCTAGATATTGCGATC 60.455 42.308 0.00 0.00 42.62 3.69
673 697 5.347342 AGTATGCTAGATATTGCGATCTGC 58.653 41.667 0.00 3.07 46.70 4.26
696 720 7.877003 TGCGATATCCTAAGTTTTTGTTCAAA 58.123 30.769 0.00 0.00 0.00 2.69
752 776 2.676463 GCCAACCTCACAAAAAGTTGCA 60.676 45.455 0.00 0.00 38.58 4.08
754 778 3.370672 CCAACCTCACAAAAAGTTGCAAC 59.629 43.478 22.17 22.17 38.58 4.17
815 852 7.463544 TGATGATTGTCGTGATTGTAAATGAC 58.536 34.615 0.00 0.00 33.72 3.06
848 885 7.880160 TTGATCAAAATCGTGATAGGGATTT 57.120 32.000 5.45 0.00 42.87 2.17
948 985 2.413765 CGCAAAGGATGTGAAGCTCAAG 60.414 50.000 0.00 0.00 42.32 3.02
954 991 3.817647 AGGATGTGAAGCTCAAGTTGAAC 59.182 43.478 7.06 2.23 0.00 3.18
977 1014 4.272489 CCTGATGGCCATTTCAACTTCTA 58.728 43.478 21.84 0.00 0.00 2.10
983 1020 4.237724 GGCCATTTCAACTTCTAAGCAAC 58.762 43.478 0.00 0.00 0.00 4.17
991 1028 0.744771 CTTCTAAGCAACGGCCCCTC 60.745 60.000 0.00 0.00 42.56 4.30
1034 1071 3.777106 TGACCTTGAGCTCTTTGATGT 57.223 42.857 16.19 3.58 0.00 3.06
1067 1104 9.038072 TGTTGAGGTTGGTGTCTATAATTACTA 57.962 33.333 0.00 0.00 0.00 1.82
1093 1132 1.142667 TGTCATCTTCTTGGGTGCACA 59.857 47.619 20.43 0.00 0.00 4.57
1230 1275 2.233271 CTGCTCAAGAAGGAAGGCAAA 58.767 47.619 0.00 0.00 0.00 3.68
1304 1349 4.461431 TGAAGACGCTGGATGTAAGTTCTA 59.539 41.667 0.00 0.00 0.00 2.10
1379 1430 4.390297 GTGAACTGACCTCAAGTTATCTGC 59.610 45.833 0.00 0.00 0.00 4.26
1463 1514 7.915923 TCTCTAGTGATGAAGTAAATGTTAGCG 59.084 37.037 0.00 0.00 0.00 4.26
1500 1552 1.985473 TGTGTTTGCAGAAGCTGGAT 58.015 45.000 0.00 0.00 42.74 3.41
1537 1601 3.873361 TGACGATGATGAGATTTTGGAGC 59.127 43.478 0.00 0.00 0.00 4.70
1546 1610 6.378848 TGATGAGATTTTGGAGCATGATGAAA 59.621 34.615 0.00 0.00 0.00 2.69
1562 1626 5.970592 TGATGAAAACAATGTGGTTGACAA 58.029 33.333 0.00 0.00 40.37 3.18
1575 1639 4.037446 GTGGTTGACAATGCTAACAAAGGA 59.963 41.667 0.00 0.00 0.00 3.36
1820 1888 7.369803 TCTTCAGTGTTGCTTTCATAATCTC 57.630 36.000 0.00 0.00 0.00 2.75
1856 1924 0.531974 GCCTGTGGAAGTGTCGAACA 60.532 55.000 0.00 0.00 0.00 3.18
1898 1966 3.970721 TCGAGGCGACTGTCGTAA 58.029 55.556 28.38 9.47 44.43 3.18
1899 1967 1.499056 TCGAGGCGACTGTCGTAAC 59.501 57.895 28.38 19.34 44.43 2.50
1900 1968 0.952497 TCGAGGCGACTGTCGTAACT 60.952 55.000 28.38 23.05 44.43 2.24
1901 1969 0.520827 CGAGGCGACTGTCGTAACTC 60.521 60.000 28.38 27.18 44.43 3.01
1906 1974 3.442977 AGGCGACTGTCGTAACTCTTAAT 59.557 43.478 28.38 3.29 42.81 1.40
1929 1997 6.114187 TCATCAGTTCCAAGAACAGTACAT 57.886 37.500 9.92 0.00 0.00 2.29
1964 2054 4.454504 TCGGCCTTCTCTTTTGTGAATTAC 59.545 41.667 0.00 0.00 32.42 1.89
2016 2270 2.160813 GTGAAGTCTGGTCTCGACTCTC 59.839 54.545 0.00 0.00 40.65 3.20
2043 2297 8.585018 GGATATCGAAAATGGATTTTATGGGTT 58.415 33.333 0.00 0.00 39.86 4.11
2065 2320 7.200455 GGTTGTACTGTTTGCTGAACTAATTT 58.800 34.615 0.00 0.00 39.08 1.82
2073 2328 7.264221 TGTTTGCTGAACTAATTTCATGTTGT 58.736 30.769 0.00 0.00 43.54 3.32
2098 2353 5.525012 TGTAAATGCAGCTGATGTAGATGTC 59.475 40.000 20.43 0.00 44.58 3.06
2159 2414 0.465460 TGCGGGTGAAGAAGCAAAGT 60.465 50.000 0.00 0.00 36.60 2.66
2185 2440 0.536687 AGATTGGAGGCGATGGCATG 60.537 55.000 3.81 0.00 42.47 4.06
2202 2465 4.338964 TGGCATGGTTACAATGATGATCAC 59.661 41.667 3.54 0.00 0.00 3.06
2284 2553 0.039527 GTGTTGGTAGCTTTTGGCCG 60.040 55.000 0.00 0.00 43.05 6.13
2312 2581 1.001048 TCTGTAGTGTTTGACGGACGG 60.001 52.381 0.00 0.00 0.00 4.79
2315 2584 0.598158 TAGTGTTTGACGGACGGCAC 60.598 55.000 0.00 0.00 29.74 5.01
2335 2604 3.012518 ACTGCTGTGCATTCTGTTATCC 58.987 45.455 0.00 0.00 38.13 2.59
2337 2606 3.011818 TGCTGTGCATTCTGTTATCCTG 58.988 45.455 0.00 0.00 31.71 3.86
2458 2728 5.402054 ACATGAAGGGCCTATTTGGATTA 57.598 39.130 6.41 0.00 38.35 1.75
2459 2729 5.969086 ACATGAAGGGCCTATTTGGATTAT 58.031 37.500 6.41 0.00 38.35 1.28
2475 2745 4.202461 TGGATTATAGCCTAAGGTTGCCAG 60.202 45.833 0.00 0.00 0.00 4.85
2496 2766 2.344025 CCCTAACTTTAGTCACGCCAC 58.656 52.381 0.00 0.00 0.00 5.01
2502 2772 4.267349 ACTTTAGTCACGCCACAGTATT 57.733 40.909 0.00 0.00 0.00 1.89
2516 2786 4.881273 CCACAGTATTTTAGGCAGTGCATA 59.119 41.667 18.61 12.12 0.00 3.14
2522 2792 7.433131 CAGTATTTTAGGCAGTGCATATGTTTG 59.567 37.037 18.61 5.02 0.00 2.93
2523 2793 5.720371 TTTTAGGCAGTGCATATGTTTGT 57.280 34.783 18.61 0.00 0.00 2.83
2531 2801 5.406175 GCAGTGCATATGTTTGTTTCATTGT 59.594 36.000 11.09 0.00 0.00 2.71
2557 2827 2.237393 TGTGGCTTGCCACATTTTTC 57.763 45.000 35.06 14.63 44.45 2.29
2572 2842 4.396166 ACATTTTTCTAGCTTCATGGTCCG 59.604 41.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.810755 GTAAAAGGAAGCCAACGAGGG 59.189 52.381 0.00 0.00 38.09 4.30
3 4 1.463444 CGTAAAAGGAAGCCAACGAGG 59.537 52.381 0.00 0.00 41.84 4.63
4 5 1.136057 GCGTAAAAGGAAGCCAACGAG 60.136 52.381 0.00 0.00 32.35 4.18
5 6 0.869730 GCGTAAAAGGAAGCCAACGA 59.130 50.000 0.00 0.00 32.35 3.85
6 7 3.378013 GCGTAAAAGGAAGCCAACG 57.622 52.632 0.00 0.00 0.00 4.10
11 12 1.858372 TTGCGGGCGTAAAAGGAAGC 61.858 55.000 0.00 0.00 0.00 3.86
22 23 2.504681 GCAAGAATGTTGCGGGCG 60.505 61.111 0.00 0.00 35.58 6.13
35 36 0.038159 AGACGGAGGAAACGAGCAAG 60.038 55.000 0.00 0.00 34.93 4.01
42 43 1.615165 GGAGGGGAGACGGAGGAAAC 61.615 65.000 0.00 0.00 0.00 2.78
105 106 1.638467 GCGCGAGTTATTGCTCCTG 59.362 57.895 12.10 0.00 33.18 3.86
112 113 1.616620 TTTCGTACGCGCGAGTTATT 58.383 45.000 39.36 16.04 42.10 1.40
121 122 1.323534 CTGGAGGAAATTTCGTACGCG 59.676 52.381 16.29 3.53 39.92 6.01
126 127 6.488683 TCATGTTTTACTGGAGGAAATTTCGT 59.511 34.615 12.98 12.98 0.00 3.85
152 153 1.276145 GATCGCGAGCGGTTATCACC 61.276 60.000 16.66 0.00 40.16 4.02
153 154 1.276145 GGATCGCGAGCGGTTATCAC 61.276 60.000 19.19 0.00 40.25 3.06
167 168 1.746727 CGCAACGCAGAGAAGGATCG 61.747 60.000 0.00 0.00 0.00 3.69
181 182 2.292103 AGAATGAGAGAGAGCGCAAC 57.708 50.000 11.47 2.78 0.00 4.17
182 183 2.232208 TCAAGAATGAGAGAGAGCGCAA 59.768 45.455 11.47 0.00 0.00 4.85
188 189 7.657023 TGAATCTGATCAAGAATGAGAGAGA 57.343 36.000 0.00 0.00 39.39 3.10
195 196 5.205565 CGCACATGAATCTGATCAAGAATG 58.794 41.667 0.00 0.00 38.79 2.67
286 305 9.970553 ACAAGACCATATGCAGAATCATATAAT 57.029 29.630 0.00 0.00 37.50 1.28
292 311 6.594744 ACATACAAGACCATATGCAGAATCA 58.405 36.000 0.00 0.00 32.92 2.57
313 332 7.709601 TGGAGGGAGTACATACTATATGACAT 58.290 38.462 2.88 0.00 36.50 3.06
321 340 3.730594 TGGGATGGAGGGAGTACATACTA 59.269 47.826 0.00 0.00 36.50 1.82
322 341 2.522705 TGGGATGGAGGGAGTACATACT 59.477 50.000 0.00 0.00 39.71 2.12
323 342 2.972348 TGGGATGGAGGGAGTACATAC 58.028 52.381 0.00 0.00 0.00 2.39
324 343 3.717507 TTGGGATGGAGGGAGTACATA 57.282 47.619 0.00 0.00 0.00 2.29
325 344 2.587060 TTGGGATGGAGGGAGTACAT 57.413 50.000 0.00 0.00 0.00 2.29
326 345 2.352561 TTTGGGATGGAGGGAGTACA 57.647 50.000 0.00 0.00 0.00 2.90
327 346 3.953542 ATTTTGGGATGGAGGGAGTAC 57.046 47.619 0.00 0.00 0.00 2.73
328 347 5.043762 ACTTATTTTGGGATGGAGGGAGTA 58.956 41.667 0.00 0.00 0.00 2.59
329 348 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
330 349 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
331 350 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
332 351 3.981212 ACACTTATTTTGGGATGGAGGG 58.019 45.455 0.00 0.00 0.00 4.30
333 352 5.480073 TGAAACACTTATTTTGGGATGGAGG 59.520 40.000 0.00 0.00 0.00 4.30
334 353 6.588719 TGAAACACTTATTTTGGGATGGAG 57.411 37.500 0.00 0.00 0.00 3.86
335 354 6.553100 AGTTGAAACACTTATTTTGGGATGGA 59.447 34.615 0.00 0.00 0.00 3.41
336 355 6.758254 AGTTGAAACACTTATTTTGGGATGG 58.242 36.000 0.00 0.00 0.00 3.51
337 356 8.550376 CAAAGTTGAAACACTTATTTTGGGATG 58.450 33.333 0.00 0.00 35.87 3.51
338 357 7.226523 GCAAAGTTGAAACACTTATTTTGGGAT 59.773 33.333 0.00 0.00 35.87 3.85
339 358 6.536941 GCAAAGTTGAAACACTTATTTTGGGA 59.463 34.615 0.00 0.00 35.87 4.37
340 359 6.314896 TGCAAAGTTGAAACACTTATTTTGGG 59.685 34.615 0.00 0.00 35.87 4.12
341 360 7.064490 AGTGCAAAGTTGAAACACTTATTTTGG 59.936 33.333 0.00 0.00 38.38 3.28
342 361 7.962917 AGTGCAAAGTTGAAACACTTATTTTG 58.037 30.769 0.00 0.00 38.38 2.44
343 362 9.646427 TTAGTGCAAAGTTGAAACACTTATTTT 57.354 25.926 7.72 0.00 41.56 1.82
344 363 9.083080 GTTAGTGCAAAGTTGAAACACTTATTT 57.917 29.630 7.72 0.00 41.56 1.40
345 364 8.466798 AGTTAGTGCAAAGTTGAAACACTTATT 58.533 29.630 7.72 0.00 41.56 1.40
346 365 7.996385 AGTTAGTGCAAAGTTGAAACACTTAT 58.004 30.769 7.72 0.00 41.56 1.73
347 366 7.385778 AGTTAGTGCAAAGTTGAAACACTTA 57.614 32.000 7.72 0.00 41.56 2.24
348 367 6.267496 AGTTAGTGCAAAGTTGAAACACTT 57.733 33.333 7.72 0.00 41.56 3.16
349 368 5.897377 AGTTAGTGCAAAGTTGAAACACT 57.103 34.783 0.00 0.00 43.60 3.55
350 369 6.944557 AAAGTTAGTGCAAAGTTGAAACAC 57.055 33.333 0.00 0.00 0.00 3.32
351 370 7.822658 ACTAAAGTTAGTGCAAAGTTGAAACA 58.177 30.769 2.91 0.00 42.13 2.83
352 371 9.218359 GTACTAAAGTTAGTGCAAAGTTGAAAC 57.782 33.333 12.92 0.00 43.22 2.78
353 372 9.169592 AGTACTAAAGTTAGTGCAAAGTTGAAA 57.830 29.630 17.86 0.00 45.23 2.69
354 373 8.726870 AGTACTAAAGTTAGTGCAAAGTTGAA 57.273 30.769 17.86 0.00 45.23 2.69
355 374 7.440255 GGAGTACTAAAGTTAGTGCAAAGTTGA 59.560 37.037 17.86 0.00 45.23 3.18
356 375 7.307811 GGGAGTACTAAAGTTAGTGCAAAGTTG 60.308 40.741 17.86 0.00 45.23 3.16
357 376 6.709397 GGGAGTACTAAAGTTAGTGCAAAGTT 59.291 38.462 17.86 1.27 45.23 2.66
358 377 6.042897 AGGGAGTACTAAAGTTAGTGCAAAGT 59.957 38.462 17.86 1.65 45.23 2.66
359 378 6.465084 AGGGAGTACTAAAGTTAGTGCAAAG 58.535 40.000 17.86 0.00 45.23 2.77
360 379 6.429521 AGGGAGTACTAAAGTTAGTGCAAA 57.570 37.500 17.86 0.00 45.23 3.68
361 380 5.046807 GGAGGGAGTACTAAAGTTAGTGCAA 60.047 44.000 17.86 0.00 45.23 4.08
362 381 4.465305 GGAGGGAGTACTAAAGTTAGTGCA 59.535 45.833 17.86 0.00 45.23 4.57
363 382 4.710865 AGGAGGGAGTACTAAAGTTAGTGC 59.289 45.833 12.92 11.59 43.44 4.40
364 383 5.360429 GGAGGAGGGAGTACTAAAGTTAGTG 59.640 48.000 12.92 0.00 43.44 2.74
365 384 5.517924 GGAGGAGGGAGTACTAAAGTTAGT 58.482 45.833 8.67 8.67 45.39 2.24
366 385 4.579753 CGGAGGAGGGAGTACTAAAGTTAG 59.420 50.000 0.00 0.00 36.82 2.34
367 386 4.530875 CGGAGGAGGGAGTACTAAAGTTA 58.469 47.826 0.00 0.00 0.00 2.24
368 387 3.363627 CGGAGGAGGGAGTACTAAAGTT 58.636 50.000 0.00 0.00 0.00 2.66
369 388 3.015675 CGGAGGAGGGAGTACTAAAGT 57.984 52.381 0.00 0.00 0.00 2.66
385 404 2.953466 TCCGACAAGTATTTCCGGAG 57.047 50.000 3.34 0.00 43.47 4.63
386 405 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
387 406 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
388 407 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
389 408 4.766375 TCATTCCTCCGACAAGTATTTCC 58.234 43.478 0.00 0.00 0.00 3.13
390 409 6.316390 ACATTCATTCCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
391 410 6.180472 ACATTCATTCCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
392 411 5.745227 ACATTCATTCCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
393 412 5.359194 ACATTCATTCCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
394 413 4.819105 ACATTCATTCCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
395 414 3.703001 ACATTCATTCCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
396 415 5.605534 AGATACATTCATTCCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
397 416 5.614324 AGATACATTCATTCCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
398 417 6.016192 GTCTAGATACATTCATTCCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
399 418 6.383415 GTCTAGATACATTCATTCCTCCGAC 58.617 44.000 0.00 0.00 0.00 4.79
400 419 5.181433 CGTCTAGATACATTCATTCCTCCGA 59.819 44.000 0.00 0.00 0.00 4.55
401 420 5.048643 ACGTCTAGATACATTCATTCCTCCG 60.049 44.000 0.00 0.00 0.00 4.63
402 421 6.334102 ACGTCTAGATACATTCATTCCTCC 57.666 41.667 0.00 0.00 0.00 4.30
403 422 9.915629 AAATACGTCTAGATACATTCATTCCTC 57.084 33.333 0.00 0.00 0.00 3.71
452 471 9.878667 TGGAAATACTTGTCGAAGAAATACATA 57.121 29.630 0.00 0.00 39.69 2.29
453 472 8.786826 TGGAAATACTTGTCGAAGAAATACAT 57.213 30.769 0.00 0.00 39.69 2.29
454 473 8.092068 TCTGGAAATACTTGTCGAAGAAATACA 58.908 33.333 0.00 0.00 39.69 2.29
455 474 8.381387 GTCTGGAAATACTTGTCGAAGAAATAC 58.619 37.037 0.00 0.00 39.69 1.89
456 475 7.274904 CGTCTGGAAATACTTGTCGAAGAAATA 59.725 37.037 0.00 0.00 39.69 1.40
457 476 6.090898 CGTCTGGAAATACTTGTCGAAGAAAT 59.909 38.462 0.00 0.00 39.69 2.17
458 477 5.404366 CGTCTGGAAATACTTGTCGAAGAAA 59.596 40.000 0.00 0.00 39.69 2.52
459 478 4.921515 CGTCTGGAAATACTTGTCGAAGAA 59.078 41.667 0.00 0.00 39.69 2.52
460 479 4.482386 CGTCTGGAAATACTTGTCGAAGA 58.518 43.478 0.00 0.00 32.98 2.87
461 480 3.612860 CCGTCTGGAAATACTTGTCGAAG 59.387 47.826 0.00 0.00 37.49 3.79
462 481 3.256383 TCCGTCTGGAAATACTTGTCGAA 59.744 43.478 0.00 0.00 42.85 3.71
463 482 2.821378 TCCGTCTGGAAATACTTGTCGA 59.179 45.455 0.00 0.00 42.85 4.20
464 483 3.179830 CTCCGTCTGGAAATACTTGTCG 58.820 50.000 0.00 0.00 45.87 4.35
465 484 3.522553 CCTCCGTCTGGAAATACTTGTC 58.477 50.000 0.00 0.00 45.87 3.18
466 485 2.236395 CCCTCCGTCTGGAAATACTTGT 59.764 50.000 0.00 0.00 45.87 3.16
467 486 2.500098 TCCCTCCGTCTGGAAATACTTG 59.500 50.000 0.00 0.00 45.87 3.16
468 487 2.766828 CTCCCTCCGTCTGGAAATACTT 59.233 50.000 0.00 0.00 45.87 2.24
469 488 2.292323 ACTCCCTCCGTCTGGAAATACT 60.292 50.000 0.00 0.00 45.87 2.12
470 489 2.108970 ACTCCCTCCGTCTGGAAATAC 58.891 52.381 0.00 0.00 45.87 1.89
471 490 2.544844 ACTCCCTCCGTCTGGAAATA 57.455 50.000 0.00 0.00 45.87 1.40
472 491 2.108970 GTACTCCCTCCGTCTGGAAAT 58.891 52.381 0.00 0.00 45.87 2.17
473 492 1.203087 TGTACTCCCTCCGTCTGGAAA 60.203 52.381 0.00 0.00 45.87 3.13
474 493 0.406750 TGTACTCCCTCCGTCTGGAA 59.593 55.000 0.00 0.00 45.87 3.53
475 494 0.406750 TTGTACTCCCTCCGTCTGGA 59.593 55.000 0.00 0.00 43.88 3.86
476 495 1.204941 CTTTGTACTCCCTCCGTCTGG 59.795 57.143 0.00 0.00 0.00 3.86
477 496 1.893801 ACTTTGTACTCCCTCCGTCTG 59.106 52.381 0.00 0.00 0.00 3.51
478 497 2.299297 CAACTTTGTACTCCCTCCGTCT 59.701 50.000 0.00 0.00 0.00 4.18
479 498 2.036862 ACAACTTTGTACTCCCTCCGTC 59.963 50.000 0.00 0.00 40.16 4.79
480 499 2.044758 ACAACTTTGTACTCCCTCCGT 58.955 47.619 0.00 0.00 40.16 4.69
481 500 2.833631 ACAACTTTGTACTCCCTCCG 57.166 50.000 0.00 0.00 40.16 4.63
498 517 8.983702 AAAATAAGTGTCTTAACCTTGGTACA 57.016 30.769 0.00 0.00 0.00 2.90
500 519 9.729281 CCTAAAATAAGTGTCTTAACCTTGGTA 57.271 33.333 0.00 0.00 0.00 3.25
501 520 8.442374 TCCTAAAATAAGTGTCTTAACCTTGGT 58.558 33.333 0.00 0.00 0.00 3.67
502 521 8.727910 GTCCTAAAATAAGTGTCTTAACCTTGG 58.272 37.037 0.00 0.00 0.00 3.61
503 522 8.440833 CGTCCTAAAATAAGTGTCTTAACCTTG 58.559 37.037 0.00 0.00 0.00 3.61
504 523 7.605309 CCGTCCTAAAATAAGTGTCTTAACCTT 59.395 37.037 0.00 0.00 0.00 3.50
505 524 7.038799 TCCGTCCTAAAATAAGTGTCTTAACCT 60.039 37.037 0.00 0.00 0.00 3.50
506 525 7.099120 TCCGTCCTAAAATAAGTGTCTTAACC 58.901 38.462 0.00 0.00 0.00 2.85
507 526 7.277319 CCTCCGTCCTAAAATAAGTGTCTTAAC 59.723 40.741 0.00 0.00 0.00 2.01
508 527 7.038799 ACCTCCGTCCTAAAATAAGTGTCTTAA 60.039 37.037 0.00 0.00 0.00 1.85
509 528 6.438425 ACCTCCGTCCTAAAATAAGTGTCTTA 59.562 38.462 0.00 0.00 0.00 2.10
510 529 5.247792 ACCTCCGTCCTAAAATAAGTGTCTT 59.752 40.000 0.00 0.00 0.00 3.01
511 530 4.776308 ACCTCCGTCCTAAAATAAGTGTCT 59.224 41.667 0.00 0.00 0.00 3.41
512 531 5.082251 ACCTCCGTCCTAAAATAAGTGTC 57.918 43.478 0.00 0.00 0.00 3.67
513 532 5.718607 ACTACCTCCGTCCTAAAATAAGTGT 59.281 40.000 0.00 0.00 0.00 3.55
514 533 6.218108 ACTACCTCCGTCCTAAAATAAGTG 57.782 41.667 0.00 0.00 0.00 3.16
515 534 8.544687 AATACTACCTCCGTCCTAAAATAAGT 57.455 34.615 0.00 0.00 0.00 2.24
517 536 9.646522 ACTAATACTACCTCCGTCCTAAAATAA 57.353 33.333 0.00 0.00 0.00 1.40
518 537 9.646522 AACTAATACTACCTCCGTCCTAAAATA 57.353 33.333 0.00 0.00 0.00 1.40
519 538 8.544687 AACTAATACTACCTCCGTCCTAAAAT 57.455 34.615 0.00 0.00 0.00 1.82
520 539 7.961326 AACTAATACTACCTCCGTCCTAAAA 57.039 36.000 0.00 0.00 0.00 1.52
521 540 8.494433 TCTAACTAATACTACCTCCGTCCTAAA 58.506 37.037 0.00 0.00 0.00 1.85
522 541 8.034313 TCTAACTAATACTACCTCCGTCCTAA 57.966 38.462 0.00 0.00 0.00 2.69
523 542 7.618019 TCTAACTAATACTACCTCCGTCCTA 57.382 40.000 0.00 0.00 0.00 2.94
524 543 6.506538 TCTAACTAATACTACCTCCGTCCT 57.493 41.667 0.00 0.00 0.00 3.85
525 544 6.939163 TGATCTAACTAATACTACCTCCGTCC 59.061 42.308 0.00 0.00 0.00 4.79
526 545 7.976135 TGATCTAACTAATACTACCTCCGTC 57.024 40.000 0.00 0.00 0.00 4.79
527 546 7.393796 CCATGATCTAACTAATACTACCTCCGT 59.606 40.741 0.00 0.00 0.00 4.69
528 547 7.148052 CCCATGATCTAACTAATACTACCTCCG 60.148 44.444 0.00 0.00 0.00 4.63
529 548 7.674772 ACCCATGATCTAACTAATACTACCTCC 59.325 40.741 0.00 0.00 0.00 4.30
530 549 8.653036 ACCCATGATCTAACTAATACTACCTC 57.347 38.462 0.00 0.00 0.00 3.85
531 550 8.457757 AGACCCATGATCTAACTAATACTACCT 58.542 37.037 0.00 0.00 0.00 3.08
532 551 8.524487 CAGACCCATGATCTAACTAATACTACC 58.476 40.741 0.00 0.00 0.00 3.18
533 552 8.524487 CCAGACCCATGATCTAACTAATACTAC 58.476 40.741 0.00 0.00 0.00 2.73
574 593 1.143684 ACAAGGTGCAATGTCCAGACT 59.856 47.619 0.00 0.00 0.00 3.24
575 594 1.609208 ACAAGGTGCAATGTCCAGAC 58.391 50.000 0.00 0.00 0.00 3.51
576 595 3.181445 ACTTACAAGGTGCAATGTCCAGA 60.181 43.478 4.50 0.00 0.00 3.86
577 596 3.149196 ACTTACAAGGTGCAATGTCCAG 58.851 45.455 4.50 5.57 0.00 3.86
578 597 3.222173 ACTTACAAGGTGCAATGTCCA 57.778 42.857 4.50 0.00 0.00 4.02
579 598 4.760204 AGTAACTTACAAGGTGCAATGTCC 59.240 41.667 4.50 0.00 30.02 4.02
601 621 5.567138 AAATGCGGGAGAAAGAAATACAG 57.433 39.130 0.00 0.00 0.00 2.74
623 643 9.781633 TGTGCCTAACTAAGAAATACAGTAAAA 57.218 29.630 0.00 0.00 0.00 1.52
624 644 9.781633 TTGTGCCTAACTAAGAAATACAGTAAA 57.218 29.630 0.00 0.00 0.00 2.01
657 681 5.532779 AGGATATCGCAGATCGCAATATCTA 59.467 40.000 20.02 3.36 45.12 1.98
660 684 4.662468 AGGATATCGCAGATCGCAATAT 57.338 40.909 9.58 6.54 45.12 1.28
665 689 3.495670 ACTTAGGATATCGCAGATCGC 57.504 47.619 0.00 0.23 45.12 4.58
670 694 7.072177 TGAACAAAAACTTAGGATATCGCAG 57.928 36.000 0.00 0.00 0.00 5.18
673 697 7.968405 CCCTTTGAACAAAAACTTAGGATATCG 59.032 37.037 0.00 0.00 0.00 2.92
683 707 1.472552 GCGGCCCTTTGAACAAAAACT 60.473 47.619 0.00 0.00 0.00 2.66
815 852 6.306397 TCACGATTTTGATCAAATCTCGTTG 58.694 36.000 33.88 29.29 46.20 4.10
848 885 1.269517 GGTGGCGAATGCACTCAAAAA 60.270 47.619 0.00 0.00 45.35 1.94
860 897 2.501223 CTTAGTGCTCGGGTGGCGAA 62.501 60.000 0.00 0.00 0.00 4.70
948 985 1.560505 AATGGCCATCAGGGTTCAAC 58.439 50.000 21.08 0.00 39.65 3.18
954 991 1.856629 AGTTGAAATGGCCATCAGGG 58.143 50.000 21.08 0.00 40.85 4.45
977 1014 4.351054 CAGGAGGGGCCGTTGCTT 62.351 66.667 0.00 0.00 43.43 3.91
983 1020 2.446848 ATGTCATCAGGAGGGGCCG 61.447 63.158 0.00 0.00 43.43 6.13
991 1028 2.806818 GCTCATACTGCATGTCATCAGG 59.193 50.000 13.45 0.00 35.96 3.86
1034 1071 2.290641 ACACCAACCTCAACACTGACAA 60.291 45.455 0.00 0.00 0.00 3.18
1067 1104 4.262164 GCACCCAAGAAGATGACATTTGTT 60.262 41.667 0.00 0.00 0.00 2.83
1150 1195 1.338200 GCATATAGTCCTCGGGGCAAG 60.338 57.143 0.00 0.00 0.00 4.01
1230 1275 0.474184 CCTTGAGGAACACAGGTGGT 59.526 55.000 4.24 0.00 37.39 4.16
1379 1430 0.042188 CAAAGTCACCAACTGCGACG 60.042 55.000 0.00 0.00 38.58 5.12
1441 1492 6.978659 CCTCGCTAACATTTACTTCATCACTA 59.021 38.462 0.00 0.00 0.00 2.74
1463 1514 3.319122 ACACAAAGAACAATGGAAGCCTC 59.681 43.478 0.00 0.00 0.00 4.70
1500 1552 1.119684 CGTCATCACCACCTCCCATA 58.880 55.000 0.00 0.00 0.00 2.74
1537 1601 5.984323 TGTCAACCACATTGTTTTCATCATG 59.016 36.000 0.00 0.00 39.54 3.07
1546 1610 5.163468 TGTTAGCATTGTCAACCACATTGTT 60.163 36.000 0.00 0.00 38.25 2.83
1562 1626 6.604795 ACATCATAAGCTTCCTTTGTTAGCAT 59.395 34.615 0.00 0.00 37.37 3.79
1609 1673 1.064758 ACAGGCATATGCTTCCCGAAA 60.065 47.619 26.12 0.00 41.70 3.46
1612 1676 0.947244 GAACAGGCATATGCTTCCCG 59.053 55.000 26.12 10.52 41.70 5.14
1777 1845 8.163408 ACTGAAGATATGTCTATGCTACTCTCT 58.837 37.037 0.00 0.00 33.30 3.10
1820 1888 3.181451 ACAGGCATGTGTATGTGATAGGG 60.181 47.826 1.71 0.00 38.57 3.53
1856 1924 6.321181 ACTTACATTGAACAACATTGGACAGT 59.679 34.615 0.00 0.00 35.12 3.55
1864 1932 4.154195 GCCTCGACTTACATTGAACAACAT 59.846 41.667 0.00 0.00 0.00 2.71
1895 1963 9.436957 TTCTTGGAACTGATGATTAAGAGTTAC 57.563 33.333 0.00 0.00 30.97 2.50
1898 1966 7.453393 TGTTCTTGGAACTGATGATTAAGAGT 58.547 34.615 10.98 0.00 0.00 3.24
1899 1967 7.605691 ACTGTTCTTGGAACTGATGATTAAGAG 59.394 37.037 18.96 5.01 0.00 2.85
1900 1968 7.453393 ACTGTTCTTGGAACTGATGATTAAGA 58.547 34.615 18.96 0.00 0.00 2.10
1901 1969 7.678947 ACTGTTCTTGGAACTGATGATTAAG 57.321 36.000 18.96 5.95 0.00 1.85
1906 1974 5.545063 TGTACTGTTCTTGGAACTGATGA 57.455 39.130 18.96 6.04 0.00 2.92
1929 1997 1.549170 GAAGGCCGACCAAAGTCTCTA 59.451 52.381 0.00 0.00 41.16 2.43
2016 2270 7.094377 ACCCATAAAATCCATTTTCGATATCCG 60.094 37.037 0.45 0.00 40.24 4.18
2043 2297 7.561021 TGAAATTAGTTCAGCAAACAGTACA 57.439 32.000 0.00 0.00 41.47 2.90
2065 2320 4.277921 TCAGCTGCATTTACAACAACATGA 59.722 37.500 9.47 0.00 0.00 3.07
2073 2328 5.882000 ACATCTACATCAGCTGCATTTACAA 59.118 36.000 9.47 0.00 0.00 2.41
2098 2353 2.124693 GCTCCCCTCCTCTGTCTCG 61.125 68.421 0.00 0.00 0.00 4.04
2143 2398 5.705609 TTTATGACTTTGCTTCTTCACCC 57.294 39.130 0.00 0.00 0.00 4.61
2159 2414 4.136796 CCATCGCCTCCAATCTTTTATGA 58.863 43.478 0.00 0.00 0.00 2.15
2185 2440 6.459257 GATCTCGTGATCATCATTGTAACC 57.541 41.667 19.80 0.00 46.20 2.85
2202 2465 5.060506 ACCAGTGTCTAGATACAGATCTCG 58.939 45.833 20.24 3.65 41.75 4.04
2284 2553 2.504175 TCAAACACTACAGATAGCCCCC 59.496 50.000 0.00 0.00 30.75 5.40
2315 2584 3.064958 CAGGATAACAGAATGCACAGCAG 59.935 47.826 0.00 0.00 43.65 4.24
2327 2596 5.695851 AAACAAGAAGTGCAGGATAACAG 57.304 39.130 0.00 0.00 0.00 3.16
2335 2604 6.428159 AGGTCTACAATAAACAAGAAGTGCAG 59.572 38.462 0.00 0.00 0.00 4.41
2337 2606 6.603095 CAGGTCTACAATAAACAAGAAGTGC 58.397 40.000 0.00 0.00 0.00 4.40
2377 2647 1.129251 CGTGACACCACAATCTCATGC 59.871 52.381 0.00 0.00 43.34 4.06
2458 2728 0.183731 GGCTGGCAACCTTAGGCTAT 59.816 55.000 0.00 0.00 34.52 2.97
2459 2729 1.607612 GGCTGGCAACCTTAGGCTA 59.392 57.895 0.00 0.00 34.52 3.93
2475 2745 1.338389 TGGCGTGACTAAAGTTAGGGC 60.338 52.381 12.31 12.31 42.41 5.19
2496 2766 6.624352 ACATATGCACTGCCTAAAATACTG 57.376 37.500 1.58 0.00 0.00 2.74
2502 2772 5.720371 AACAAACATATGCACTGCCTAAA 57.280 34.783 1.58 0.00 0.00 1.85
2516 2786 6.339730 ACATGTGTGACAATGAAACAAACAT 58.660 32.000 0.00 0.00 41.34 2.71
2552 2822 2.747446 GCGGACCATGAAGCTAGAAAAA 59.253 45.455 0.00 0.00 0.00 1.94
2556 2826 1.123077 ATGCGGACCATGAAGCTAGA 58.877 50.000 0.00 0.00 31.48 2.43
2557 2827 3.694364 ATGCGGACCATGAAGCTAG 57.306 52.632 0.00 0.00 31.48 3.42


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

AutoCloner maintained by Alex Coulton.