Multiple sequence alignment - TraesCS7B01G369800

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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 TraesCS7B01G369800 chr7B 100.000 3553 0 0 1 3553 634569598 634566046 0.000000e+00 6562.0
1 TraesCS7B01G369800 chr7B 97.038 3005 78 3 549 3553 289504810 289507803 0.000000e+00 5046.0
2 TraesCS7B01G369800 chr7B 100.000 43 0 0 885 927 721578206 721578164 2.940000e-11 80.5
3 TraesCS7B01G369800 chr7A 91.156 1142 29 20 928 2000 536156673 536155535 0.000000e+00 1483.0
4 TraesCS7B01G369800 chr7A 94.910 334 7 2 3227 3553 536155537 536155207 6.800000e-142 514.0
5 TraesCS7B01G369800 chr7A 94.895 333 8 5 639 971 536156986 536156663 2.450000e-141 512.0
6 TraesCS7B01G369800 chr7A 81.818 121 18 2 149 269 664284312 664284196 8.120000e-17 99.0
7 TraesCS7B01G369800 chr7A 90.141 71 5 2 1748 1817 526126431 526126500 1.360000e-14 91.6
8 TraesCS7B01G369800 chr2A 90.455 1142 37 15 928 2000 24010608 24011746 0.000000e+00 1439.0
9 TraesCS7B01G369800 chr2A 87.511 1153 91 19 2085 3227 463732996 463734105 0.000000e+00 1282.0
10 TraesCS7B01G369800 chr2A 94.910 334 7 2 3227 3553 24011744 24012074 6.800000e-142 514.0
11 TraesCS7B01G369800 chr2A 93.548 341 13 5 631 971 24010287 24010618 1.900000e-137 499.0
12 TraesCS7B01G369800 chr2A 87.536 345 32 3 3212 3549 463734486 463734826 4.300000e-104 388.0
13 TraesCS7B01G369800 chr2A 89.091 275 30 0 1816 2090 463732687 463732961 3.400000e-90 342.0
14 TraesCS7B01G369800 chr7D 87.663 1151 93 16 2085 3227 214637721 214636612 0.000000e+00 1293.0
15 TraesCS7B01G369800 chr7D 82.197 1393 157 35 2136 3503 106978188 106976862 0.000000e+00 1114.0
16 TraesCS7B01G369800 chr7D 93.009 329 23 0 1 329 574681395 574681067 6.900000e-132 481.0
17 TraesCS7B01G369800 chr7D 90.234 256 25 0 1835 2090 214638011 214637756 5.680000e-88 335.0
18 TraesCS7B01G369800 chr7D 85.759 316 33 4 3243 3549 214636389 214636077 1.230000e-84 324.0
19 TraesCS7B01G369800 chr7D 91.630 227 10 2 326 550 574678524 574678305 4.460000e-79 305.0
20 TraesCS7B01G369800 chr6B 96.648 716 14 2 2845 3553 35065012 35065724 0.000000e+00 1181.0
21 TraesCS7B01G369800 chr2B 96.369 716 16 2 2845 3553 738171312 738170600 0.000000e+00 1170.0
22 TraesCS7B01G369800 chr2B 86.494 385 38 8 549 928 37543336 37542961 9.180000e-111 411.0
23 TraesCS7B01G369800 chr2B 86.538 260 29 6 549 806 480156273 480156018 7.510000e-72 281.0
24 TraesCS7B01G369800 chr2B 86.770 257 27 7 552 805 480140604 480140352 2.700000e-71 279.0
25 TraesCS7B01G369800 chr2B 86.770 257 27 7 552 805 480144306 480144054 2.700000e-71 279.0
26 TraesCS7B01G369800 chr2B 82.645 121 12 6 325 440 500185904 500185788 8.120000e-17 99.0
27 TraesCS7B01G369800 chr2B 93.023 43 3 0 3159 3201 23345508 23345550 2.960000e-06 63.9
28 TraesCS7B01G369800 chr3A 84.586 1064 126 18 2511 3549 650148299 650149349 0.000000e+00 1022.0
29 TraesCS7B01G369800 chr3A 81.595 163 13 10 769 928 567998690 567998838 6.230000e-23 119.0
30 TraesCS7B01G369800 chr3A 88.462 78 8 1 1747 1823 424454702 424454779 3.780000e-15 93.5
31 TraesCS7B01G369800 chr4B 89.556 766 62 6 2470 3227 386040887 386041642 0.000000e+00 955.0
32 TraesCS7B01G369800 chr4B 80.914 372 39 13 559 927 211591619 211591277 7.560000e-67 265.0
33 TraesCS7B01G369800 chr4B 83.505 291 24 8 3212 3481 386042023 386042310 2.120000e-62 250.0
34 TraesCS7B01G369800 chr4B 94.667 75 4 0 3477 3551 386045014 386045088 2.240000e-22 117.0
35 TraesCS7B01G369800 chr4B 91.045 67 6 0 1754 1820 172735557 172735491 1.360000e-14 91.6
36 TraesCS7B01G369800 chr4B 89.130 46 4 1 396 441 67498726 67498682 4.960000e-04 56.5
37 TraesCS7B01G369800 chr6A 85.558 457 50 6 2987 3428 432572946 432573401 6.950000e-127 464.0
38 TraesCS7B01G369800 chrUn 88.153 287 27 7 548 831 70952619 70952337 5.680000e-88 335.0
39 TraesCS7B01G369800 chr5D 84.775 289 35 7 546 831 254528301 254528583 7.510000e-72 281.0
40 TraesCS7B01G369800 chr1B 79.177 389 40 24 546 928 55530374 55530727 7.670000e-57 231.0
41 TraesCS7B01G369800 chr1B 100.000 44 0 0 885 928 503322209 503322166 8.180000e-12 82.4
42 TraesCS7B01G369800 chr4A 78.228 395 42 21 549 928 625000292 624999927 2.780000e-51 213.0
43 TraesCS7B01G369800 chr1A 87.356 174 21 1 2981 3153 361326934 361326761 7.780000e-47 198.0
44 TraesCS7B01G369800 chr4D 94.444 72 4 0 1749 1820 484462786 484462715 1.040000e-20 111.0
45 TraesCS7B01G369800 chr4D 91.429 70 6 0 1751 1820 112074056 112073987 2.920000e-16 97.1
46 TraesCS7B01G369800 chr2D 93.846 65 4 0 1753 1817 579827108 579827044 8.120000e-17 99.0
47 TraesCS7B01G369800 chr1D 82.203 118 16 5 325 441 45133252 45133365 2.920000e-16 97.1
48 TraesCS7B01G369800 chr1D 81.356 118 20 2 325 441 45095666 45095782 1.050000e-15 95.3
49 TraesCS7B01G369800 chr1D 81.553 103 15 3 325 426 44977239 44977338 8.180000e-12 82.4
50 TraesCS7B01G369800 chr3D 97.436 39 1 0 325 363 498235324 498235362 2.290000e-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 TraesCS7B01G369800 chr7B 634566046 634569598 3552 True 6562.000000 6562 100.000000 1 3553 1 chr7B.!!$R1 3552
1 TraesCS7B01G369800 chr7B 289504810 289507803 2993 False 5046.000000 5046 97.038000 549 3553 1 chr7B.!!$F1 3004
2 TraesCS7B01G369800 chr7A 536155207 536156986 1779 True 836.333333 1483 93.653667 639 3553 3 chr7A.!!$R2 2914
3 TraesCS7B01G369800 chr2A 24010287 24012074 1787 False 817.333333 1439 92.971000 631 3553 3 chr2A.!!$F1 2922
4 TraesCS7B01G369800 chr2A 463732687 463734826 2139 False 670.666667 1282 88.046000 1816 3549 3 chr2A.!!$F2 1733
5 TraesCS7B01G369800 chr7D 106976862 106978188 1326 True 1114.000000 1114 82.197000 2136 3503 1 chr7D.!!$R1 1367
6 TraesCS7B01G369800 chr7D 214636077 214638011 1934 True 650.666667 1293 87.885333 1835 3549 3 chr7D.!!$R2 1714
7 TraesCS7B01G369800 chr7D 574678305 574681395 3090 True 393.000000 481 92.319500 1 550 2 chr7D.!!$R3 549
8 TraesCS7B01G369800 chr6B 35065012 35065724 712 False 1181.000000 1181 96.648000 2845 3553 1 chr6B.!!$F1 708
9 TraesCS7B01G369800 chr2B 738170600 738171312 712 True 1170.000000 1170 96.369000 2845 3553 1 chr2B.!!$R4 708
10 TraesCS7B01G369800 chr2B 480140352 480144306 3954 True 279.000000 279 86.770000 552 805 2 chr2B.!!$R5 253
11 TraesCS7B01G369800 chr3A 650148299 650149349 1050 False 1022.000000 1022 84.586000 2511 3549 1 chr3A.!!$F3 1038
12 TraesCS7B01G369800 chr4B 386040887 386045088 4201 False 440.666667 955 89.242667 2470 3551 3 chr4B.!!$F1 1081

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
329 330 0.114364 TGGCTAGAGGGCGGATGATA 59.886 55.000 0.0 0.0 44.11 2.15 F
478 479 0.375454 CGGCAACACGTTTCTTCACA 59.625 50.000 0.0 0.0 0.00 3.58 F
1331 1389 0.964358 CCGTCTCCAGGTACGTCCTT 60.964 60.000 13.7 0.0 45.67 3.36 F
1629 2335 3.111853 TCTTCAGTTGACGCACTTGAT 57.888 42.857 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1259 1.456705 GACTCCGCTCCTCCTCCAT 60.457 63.158 0.00 0.00 0.00 3.41 R
1602 2308 2.031769 TGCGTCAACTGAAGAATTGCAG 60.032 45.455 0.00 0.00 38.10 4.41 R
2547 3725 3.822735 ACACTGGTCAAAAGTGATCATGG 59.177 43.478 10.35 0.00 44.00 3.66 R
3438 8622 1.938016 GCCCAAAAACTGAGCATGCAG 60.938 52.381 21.98 12.16 41.63 4.41 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
24 25 2.045926 CTGAACGCCCCCTTCCTG 60.046 66.667 0.00 0.00 0.00 3.86
41 42 0.460284 CTGCCTCTTCATTACCGCGT 60.460 55.000 4.92 0.00 0.00 6.01
51 52 3.961225 TTACCGCGTGCTCCCCCTA 62.961 63.158 4.92 0.00 0.00 3.53
85 86 1.376037 GCATACCATAGCCGGCTCC 60.376 63.158 36.73 8.33 0.00 4.70
141 142 3.952628 GGTTGAGACCGCCGAAGGG 62.953 68.421 0.00 0.00 42.43 3.95
158 159 4.357947 GCACCGCGACAGAGACCA 62.358 66.667 8.23 0.00 0.00 4.02
177 178 0.686769 ATCCTCCACGTACCCACTCC 60.687 60.000 0.00 0.00 0.00 3.85
197 198 2.630158 CTGAGCTCATCCCTTTGACTG 58.370 52.381 18.63 0.00 0.00 3.51
211 212 4.021981 CCTTTGACTGTTCCCTTCCATTTC 60.022 45.833 0.00 0.00 0.00 2.17
215 216 0.610785 TGTTCCCTTCCATTTCGCCC 60.611 55.000 0.00 0.00 0.00 6.13
219 220 1.609783 CCTTCCATTTCGCCCTCCT 59.390 57.895 0.00 0.00 0.00 3.69
221 222 0.253044 CTTCCATTTCGCCCTCCTGA 59.747 55.000 0.00 0.00 0.00 3.86
222 223 0.918983 TTCCATTTCGCCCTCCTGAT 59.081 50.000 0.00 0.00 0.00 2.90
286 287 1.134521 TCATGATAAACGCGGCTTCCT 60.135 47.619 12.47 0.00 0.00 3.36
303 304 1.430632 CTGCCACCATCGATGCAAC 59.569 57.895 20.25 9.13 32.58 4.17
329 330 0.114364 TGGCTAGAGGGCGGATGATA 59.886 55.000 0.00 0.00 44.11 2.15
330 331 1.273267 TGGCTAGAGGGCGGATGATAT 60.273 52.381 0.00 0.00 44.11 1.63
332 333 3.235200 GGCTAGAGGGCGGATGATATAT 58.765 50.000 0.00 0.00 0.00 0.86
334 335 4.101741 GGCTAGAGGGCGGATGATATATTT 59.898 45.833 0.00 0.00 0.00 1.40
335 336 5.396884 GGCTAGAGGGCGGATGATATATTTT 60.397 44.000 0.00 0.00 0.00 1.82
336 337 6.116126 GCTAGAGGGCGGATGATATATTTTT 58.884 40.000 0.00 0.00 0.00 1.94
337 338 6.037610 GCTAGAGGGCGGATGATATATTTTTG 59.962 42.308 0.00 0.00 0.00 2.44
338 339 6.126863 AGAGGGCGGATGATATATTTTTGA 57.873 37.500 0.00 0.00 0.00 2.69
339 340 5.940470 AGAGGGCGGATGATATATTTTTGAC 59.060 40.000 0.00 0.00 0.00 3.18
342 343 6.721208 AGGGCGGATGATATATTTTTGACATT 59.279 34.615 0.00 0.00 0.00 2.71
343 344 7.233348 AGGGCGGATGATATATTTTTGACATTT 59.767 33.333 0.00 0.00 0.00 2.32
344 345 7.872483 GGGCGGATGATATATTTTTGACATTTT 59.128 33.333 0.00 0.00 0.00 1.82
345 346 9.906660 GGCGGATGATATATTTTTGACATTTTA 57.093 29.630 0.00 0.00 0.00 1.52
365 366 9.717942 CATTTTAGATGTAAATGTTTTTCCCCA 57.282 29.630 0.00 0.00 37.90 4.96
366 367 9.719355 ATTTTAGATGTAAATGTTTTTCCCCAC 57.281 29.630 0.00 0.00 0.00 4.61
367 368 7.841282 TTAGATGTAAATGTTTTTCCCCACA 57.159 32.000 0.00 0.00 0.00 4.17
368 369 6.739331 AGATGTAAATGTTTTTCCCCACAA 57.261 33.333 0.00 0.00 0.00 3.33
369 370 7.130681 AGATGTAAATGTTTTTCCCCACAAA 57.869 32.000 0.00 0.00 0.00 2.83
370 371 6.989759 AGATGTAAATGTTTTTCCCCACAAAC 59.010 34.615 0.00 0.00 34.09 2.93
371 372 6.049955 TGTAAATGTTTTTCCCCACAAACA 57.950 33.333 0.27 0.27 44.78 2.83
374 375 3.550437 TGTTTTTCCCCACAAACATGG 57.450 42.857 0.00 0.00 37.85 3.66
375 376 3.107601 TGTTTTTCCCCACAAACATGGA 58.892 40.909 0.00 0.00 43.02 3.41
376 377 3.118592 TGTTTTTCCCCACAAACATGGAC 60.119 43.478 0.00 0.00 43.02 4.02
377 378 2.461300 TTTCCCCACAAACATGGACA 57.539 45.000 0.00 0.00 43.02 4.02
378 379 2.461300 TTCCCCACAAACATGGACAA 57.539 45.000 0.00 0.00 43.02 3.18
379 380 2.461300 TCCCCACAAACATGGACAAA 57.539 45.000 0.00 0.00 43.02 2.83
380 381 2.969628 TCCCCACAAACATGGACAAAT 58.030 42.857 0.00 0.00 43.02 2.32
381 382 3.312890 TCCCCACAAACATGGACAAATT 58.687 40.909 0.00 0.00 43.02 1.82
382 383 3.070734 TCCCCACAAACATGGACAAATTG 59.929 43.478 0.00 0.00 43.02 2.32
383 384 3.181456 CCCCACAAACATGGACAAATTGT 60.181 43.478 0.00 0.00 43.02 2.71
384 385 3.808726 CCCACAAACATGGACAAATTGTG 59.191 43.478 2.20 15.37 46.38 3.33
385 386 3.248125 CCACAAACATGGACAAATTGTGC 59.752 43.478 10.77 10.77 45.80 4.57
386 387 3.060406 CACAAACATGGACAAATTGTGCG 60.060 43.478 12.73 2.39 41.94 5.34
387 388 3.181482 ACAAACATGGACAAATTGTGCGA 60.181 39.130 12.73 3.11 41.94 5.10
388 389 2.995466 ACATGGACAAATTGTGCGAG 57.005 45.000 12.73 9.81 41.94 5.03
389 390 1.541147 ACATGGACAAATTGTGCGAGG 59.459 47.619 12.73 7.19 41.94 4.63
390 391 1.541147 CATGGACAAATTGTGCGAGGT 59.459 47.619 12.73 0.00 41.94 3.85
391 392 1.686355 TGGACAAATTGTGCGAGGTT 58.314 45.000 12.73 0.00 41.94 3.50
392 393 2.028130 TGGACAAATTGTGCGAGGTTT 58.972 42.857 12.73 0.00 41.94 3.27
393 394 2.223688 TGGACAAATTGTGCGAGGTTTG 60.224 45.455 12.73 0.00 41.94 2.93
394 395 1.786579 GACAAATTGTGCGAGGTTTGC 59.213 47.619 2.20 0.00 35.53 3.68
395 396 1.408702 ACAAATTGTGCGAGGTTTGCT 59.591 42.857 0.00 0.00 35.53 3.91
396 397 2.159114 ACAAATTGTGCGAGGTTTGCTT 60.159 40.909 0.00 0.00 35.53 3.91
397 398 2.865551 CAAATTGTGCGAGGTTTGCTTT 59.134 40.909 0.00 0.00 0.00 3.51
398 399 2.888834 ATTGTGCGAGGTTTGCTTTT 57.111 40.000 0.00 0.00 0.00 2.27
399 400 2.202295 TTGTGCGAGGTTTGCTTTTC 57.798 45.000 0.00 0.00 0.00 2.29
400 401 1.098869 TGTGCGAGGTTTGCTTTTCA 58.901 45.000 0.00 0.00 0.00 2.69
401 402 1.474478 TGTGCGAGGTTTGCTTTTCAA 59.526 42.857 0.00 0.00 0.00 2.69
402 403 2.094494 TGTGCGAGGTTTGCTTTTCAAA 60.094 40.909 0.00 0.00 42.01 2.69
403 404 2.926838 GTGCGAGGTTTGCTTTTCAAAA 59.073 40.909 0.00 0.00 45.35 2.44
404 405 3.369451 GTGCGAGGTTTGCTTTTCAAAAA 59.631 39.130 0.00 0.00 45.35 1.94
405 406 4.033932 GTGCGAGGTTTGCTTTTCAAAAAT 59.966 37.500 0.00 0.00 45.35 1.82
406 407 4.633565 TGCGAGGTTTGCTTTTCAAAAATT 59.366 33.333 0.00 0.00 45.35 1.82
407 408 5.812642 TGCGAGGTTTGCTTTTCAAAAATTA 59.187 32.000 0.00 0.00 45.35 1.40
408 409 6.481644 TGCGAGGTTTGCTTTTCAAAAATTAT 59.518 30.769 0.00 0.00 45.35 1.28
409 410 7.653713 TGCGAGGTTTGCTTTTCAAAAATTATA 59.346 29.630 0.00 0.00 45.35 0.98
410 411 8.655970 GCGAGGTTTGCTTTTCAAAAATTATAT 58.344 29.630 0.00 0.00 45.35 0.86
440 441 7.426929 CTACATTATGAAATGGAGGCAGTAC 57.573 40.000 0.00 0.00 46.48 2.73
441 442 5.754782 ACATTATGAAATGGAGGCAGTACA 58.245 37.500 0.00 0.00 45.72 2.90
442 443 5.590259 ACATTATGAAATGGAGGCAGTACAC 59.410 40.000 0.00 0.00 45.72 2.90
443 444 3.719268 ATGAAATGGAGGCAGTACACA 57.281 42.857 0.00 0.00 0.00 3.72
444 445 3.057969 TGAAATGGAGGCAGTACACAG 57.942 47.619 0.00 0.00 0.00 3.66
445 446 2.371841 TGAAATGGAGGCAGTACACAGT 59.628 45.455 0.00 0.00 0.00 3.55
446 447 3.580895 TGAAATGGAGGCAGTACACAGTA 59.419 43.478 0.00 0.00 0.00 2.74
447 448 3.895232 AATGGAGGCAGTACACAGTAG 57.105 47.619 0.00 0.00 0.00 2.57
448 449 2.304221 TGGAGGCAGTACACAGTAGT 57.696 50.000 0.00 0.00 0.00 2.73
449 450 3.444792 TGGAGGCAGTACACAGTAGTA 57.555 47.619 0.00 0.00 0.00 1.82
450 451 3.770046 TGGAGGCAGTACACAGTAGTAA 58.230 45.455 0.00 0.00 0.00 2.24
451 452 3.762288 TGGAGGCAGTACACAGTAGTAAG 59.238 47.826 0.00 0.00 0.00 2.34
452 453 4.015084 GGAGGCAGTACACAGTAGTAAGA 58.985 47.826 0.00 0.00 0.00 2.10
453 454 4.645588 GGAGGCAGTACACAGTAGTAAGAT 59.354 45.833 0.00 0.00 0.00 2.40
454 455 5.826737 GGAGGCAGTACACAGTAGTAAGATA 59.173 44.000 0.00 0.00 0.00 1.98
455 456 6.016943 GGAGGCAGTACACAGTAGTAAGATAG 60.017 46.154 0.00 0.00 0.00 2.08
456 457 6.660800 AGGCAGTACACAGTAGTAAGATAGA 58.339 40.000 0.00 0.00 0.00 1.98
457 458 7.291566 AGGCAGTACACAGTAGTAAGATAGAT 58.708 38.462 0.00 0.00 0.00 1.98
458 459 7.780745 AGGCAGTACACAGTAGTAAGATAGATT 59.219 37.037 0.00 0.00 0.00 2.40
459 460 8.077386 GGCAGTACACAGTAGTAAGATAGATTC 58.923 40.741 0.00 0.00 0.00 2.52
460 461 7.799447 GCAGTACACAGTAGTAAGATAGATTCG 59.201 40.741 0.00 0.00 0.00 3.34
461 462 8.283992 CAGTACACAGTAGTAAGATAGATTCGG 58.716 40.741 0.00 0.00 0.00 4.30
462 463 6.074544 ACACAGTAGTAAGATAGATTCGGC 57.925 41.667 0.00 0.00 0.00 5.54
463 464 5.593095 ACACAGTAGTAAGATAGATTCGGCA 59.407 40.000 0.00 0.00 0.00 5.69
464 465 6.096423 ACACAGTAGTAAGATAGATTCGGCAA 59.904 38.462 0.00 0.00 0.00 4.52
465 466 6.418226 CACAGTAGTAAGATAGATTCGGCAAC 59.582 42.308 0.00 0.00 0.00 4.17
466 467 6.096423 ACAGTAGTAAGATAGATTCGGCAACA 59.904 38.462 0.00 0.00 0.00 3.33
467 468 6.418226 CAGTAGTAAGATAGATTCGGCAACAC 59.582 42.308 0.00 0.00 0.00 3.32
468 469 4.360563 AGTAAGATAGATTCGGCAACACG 58.639 43.478 0.00 0.00 0.00 4.49
469 470 2.961526 AGATAGATTCGGCAACACGT 57.038 45.000 0.00 0.00 34.94 4.49
470 471 3.247006 AGATAGATTCGGCAACACGTT 57.753 42.857 0.00 0.00 34.94 3.99
471 472 3.596214 AGATAGATTCGGCAACACGTTT 58.404 40.909 0.00 0.00 34.94 3.60
472 473 3.617263 AGATAGATTCGGCAACACGTTTC 59.383 43.478 0.00 0.00 34.94 2.78
473 474 1.878953 AGATTCGGCAACACGTTTCT 58.121 45.000 0.00 0.00 34.94 2.52
474 475 2.218603 AGATTCGGCAACACGTTTCTT 58.781 42.857 0.00 0.00 34.94 2.52
475 476 2.223377 AGATTCGGCAACACGTTTCTTC 59.777 45.455 0.00 0.00 34.94 2.87
476 477 1.370609 TTCGGCAACACGTTTCTTCA 58.629 45.000 0.00 0.00 34.94 3.02
477 478 0.653636 TCGGCAACACGTTTCTTCAC 59.346 50.000 0.00 0.00 34.94 3.18
478 479 0.375454 CGGCAACACGTTTCTTCACA 59.625 50.000 0.00 0.00 0.00 3.58
479 480 1.202087 CGGCAACACGTTTCTTCACAA 60.202 47.619 0.00 0.00 0.00 3.33
480 481 2.182014 GGCAACACGTTTCTTCACAAC 58.818 47.619 0.00 0.00 0.00 3.32
481 482 2.414824 GGCAACACGTTTCTTCACAACA 60.415 45.455 0.00 0.00 0.00 3.33
482 483 2.592459 GCAACACGTTTCTTCACAACAC 59.408 45.455 0.00 0.00 0.00 3.32
483 484 2.798834 ACACGTTTCTTCACAACACG 57.201 45.000 0.00 0.00 36.91 4.49
484 485 2.070783 ACACGTTTCTTCACAACACGT 58.929 42.857 0.00 0.00 44.60 4.49
485 486 3.252400 ACACGTTTCTTCACAACACGTA 58.748 40.909 0.00 0.00 41.97 3.57
486 487 3.305094 ACACGTTTCTTCACAACACGTAG 59.695 43.478 0.00 0.00 41.97 3.51
487 488 3.548668 CACGTTTCTTCACAACACGTAGA 59.451 43.478 0.00 0.00 41.97 2.59
488 489 3.549070 ACGTTTCTTCACAACACGTAGAC 59.451 43.478 0.00 0.00 42.06 2.59
489 490 3.795101 CGTTTCTTCACAACACGTAGACT 59.205 43.478 0.00 0.00 0.00 3.24
490 491 4.266976 CGTTTCTTCACAACACGTAGACTT 59.733 41.667 0.00 0.00 0.00 3.01
491 492 5.456497 CGTTTCTTCACAACACGTAGACTTA 59.544 40.000 0.00 0.00 0.00 2.24
492 493 6.143438 CGTTTCTTCACAACACGTAGACTTAT 59.857 38.462 0.00 0.00 0.00 1.73
493 494 7.324375 CGTTTCTTCACAACACGTAGACTTATA 59.676 37.037 0.00 0.00 0.00 0.98
494 495 8.636843 GTTTCTTCACAACACGTAGACTTATAG 58.363 37.037 0.00 0.00 0.00 1.31
495 496 6.320171 TCTTCACAACACGTAGACTTATAGC 58.680 40.000 0.00 0.00 0.00 2.97
496 497 5.632244 TCACAACACGTAGACTTATAGCA 57.368 39.130 0.00 0.00 0.00 3.49
497 498 5.396484 TCACAACACGTAGACTTATAGCAC 58.604 41.667 0.00 0.00 0.00 4.40
498 499 5.048573 TCACAACACGTAGACTTATAGCACA 60.049 40.000 0.00 0.00 0.00 4.57
499 500 5.805486 CACAACACGTAGACTTATAGCACAT 59.195 40.000 0.00 0.00 0.00 3.21
500 501 6.310467 CACAACACGTAGACTTATAGCACATT 59.690 38.462 0.00 0.00 0.00 2.71
501 502 7.486870 CACAACACGTAGACTTATAGCACATTA 59.513 37.037 0.00 0.00 0.00 1.90
502 503 8.030692 ACAACACGTAGACTTATAGCACATTAA 58.969 33.333 0.00 0.00 0.00 1.40
503 504 8.865978 CAACACGTAGACTTATAGCACATTAAA 58.134 33.333 0.00 0.00 0.00 1.52
504 505 9.595823 AACACGTAGACTTATAGCACATTAAAT 57.404 29.630 0.00 0.00 0.00 1.40
505 506 9.245962 ACACGTAGACTTATAGCACATTAAATC 57.754 33.333 0.00 0.00 0.00 2.17
506 507 9.244799 CACGTAGACTTATAGCACATTAAATCA 57.755 33.333 0.00 0.00 0.00 2.57
507 508 9.811995 ACGTAGACTTATAGCACATTAAATCAA 57.188 29.630 0.00 0.00 0.00 2.57
510 511 8.970859 AGACTTATAGCACATTAAATCAAGCT 57.029 30.769 0.00 0.00 36.20 3.74
511 512 8.834465 AGACTTATAGCACATTAAATCAAGCTG 58.166 33.333 0.00 0.00 33.83 4.24
512 513 8.511604 ACTTATAGCACATTAAATCAAGCTGT 57.488 30.769 0.00 0.00 33.83 4.40
513 514 8.400947 ACTTATAGCACATTAAATCAAGCTGTG 58.599 33.333 0.00 0.00 40.06 3.66
514 515 6.764308 ATAGCACATTAAATCAAGCTGTGT 57.236 33.333 0.00 0.00 39.45 3.72
515 516 5.458041 AGCACATTAAATCAAGCTGTGTT 57.542 34.783 5.33 0.00 39.45 3.32
516 517 5.464168 AGCACATTAAATCAAGCTGTGTTC 58.536 37.500 5.33 0.00 39.45 3.18
517 518 5.242393 AGCACATTAAATCAAGCTGTGTTCT 59.758 36.000 5.33 0.00 39.45 3.01
518 519 6.430925 AGCACATTAAATCAAGCTGTGTTCTA 59.569 34.615 5.33 0.00 39.45 2.10
519 520 7.121759 AGCACATTAAATCAAGCTGTGTTCTAT 59.878 33.333 5.33 0.00 39.45 1.98
520 521 7.756722 GCACATTAAATCAAGCTGTGTTCTATT 59.243 33.333 5.33 0.00 39.45 1.73
527 528 9.453572 AAATCAAGCTGTGTTCTATTATCTCAA 57.546 29.630 0.00 0.00 0.00 3.02
528 529 9.453572 AATCAAGCTGTGTTCTATTATCTCAAA 57.546 29.630 0.00 0.00 0.00 2.69
529 530 8.256611 TCAAGCTGTGTTCTATTATCTCAAAC 57.743 34.615 0.00 0.00 0.00 2.93
530 531 7.877612 TCAAGCTGTGTTCTATTATCTCAAACA 59.122 33.333 0.00 0.00 0.00 2.83
531 532 8.506437 CAAGCTGTGTTCTATTATCTCAAACAA 58.494 33.333 0.00 0.00 32.17 2.83
532 533 8.621532 AGCTGTGTTCTATTATCTCAAACAAA 57.378 30.769 0.00 0.00 32.17 2.83
533 534 8.507249 AGCTGTGTTCTATTATCTCAAACAAAC 58.493 33.333 0.00 0.00 32.17 2.93
534 535 8.507249 GCTGTGTTCTATTATCTCAAACAAACT 58.493 33.333 0.00 0.00 32.17 2.66
536 537 8.708742 TGTGTTCTATTATCTCAAACAAACTCG 58.291 33.333 0.00 0.00 32.17 4.18
537 538 8.709646 GTGTTCTATTATCTCAAACAAACTCGT 58.290 33.333 0.00 0.00 32.17 4.18
538 539 8.922676 TGTTCTATTATCTCAAACAAACTCGTC 58.077 33.333 0.00 0.00 0.00 4.20
539 540 7.736031 TCTATTATCTCAAACAAACTCGTCG 57.264 36.000 0.00 0.00 0.00 5.12
540 541 7.532571 TCTATTATCTCAAACAAACTCGTCGA 58.467 34.615 0.00 0.00 0.00 4.20
541 542 5.817616 TTATCTCAAACAAACTCGTCGAC 57.182 39.130 5.18 5.18 0.00 4.20
542 543 3.153676 TCTCAAACAAACTCGTCGACA 57.846 42.857 17.16 1.87 0.00 4.35
543 544 2.855963 TCTCAAACAAACTCGTCGACAC 59.144 45.455 17.16 0.00 0.00 3.67
544 545 1.928503 TCAAACAAACTCGTCGACACC 59.071 47.619 17.16 0.00 0.00 4.16
545 546 1.931172 CAAACAAACTCGTCGACACCT 59.069 47.619 17.16 0.00 0.00 4.00
546 547 2.304751 AACAAACTCGTCGACACCTT 57.695 45.000 17.16 0.00 0.00 3.50
547 548 1.849097 ACAAACTCGTCGACACCTTC 58.151 50.000 17.16 0.00 0.00 3.46
796 813 8.664211 AAAATTAACCAGCGAAAATTAACCAA 57.336 26.923 0.00 0.00 0.00 3.67
877 894 1.495584 AAACACTCGCACGCACGAAT 61.496 50.000 0.00 0.00 42.39 3.34
878 895 1.886861 AACACTCGCACGCACGAATC 61.887 55.000 0.00 0.00 42.39 2.52
879 896 2.088763 CACTCGCACGCACGAATCT 61.089 57.895 0.00 0.00 42.39 2.40
880 897 1.801913 ACTCGCACGCACGAATCTC 60.802 57.895 0.00 0.00 42.39 2.75
881 898 2.839438 CTCGCACGCACGAATCTCG 61.839 63.158 0.00 0.00 46.93 4.04
882 899 2.874315 CGCACGCACGAATCTCGA 60.874 61.111 2.59 0.00 43.74 4.04
883 900 2.433334 CGCACGCACGAATCTCGAA 61.433 57.895 2.59 0.00 43.74 3.71
1005 1063 2.387851 GATCGGGGGAGGAGATGGGA 62.388 65.000 0.00 0.00 0.00 4.37
1007 1065 3.037715 GGGGGAGGAGATGGGAGA 58.962 66.667 0.00 0.00 0.00 3.71
1201 1259 1.892819 CGCAAGGGAGAAGCAGAGGA 61.893 60.000 0.00 0.00 0.00 3.71
1241 1299 2.261671 GAGGAAAGCAGGCGACGA 59.738 61.111 0.00 0.00 0.00 4.20
1331 1389 0.964358 CCGTCTCCAGGTACGTCCTT 60.964 60.000 13.70 0.00 45.67 3.36
1602 2308 9.385902 CATCAACACATACGAAATCCATTAATC 57.614 33.333 0.00 0.00 0.00 1.75
1629 2335 3.111853 TCTTCAGTTGACGCACTTGAT 57.888 42.857 0.00 0.00 0.00 2.57
1716 2422 7.591421 TTAATCATGTGATGCATCCTTGAAT 57.409 32.000 23.67 19.76 35.19 2.57
2155 3214 9.282905 AGTGTTATAGGGGTATTTTGTAACCTA 57.717 33.333 0.00 0.00 35.97 3.08
2547 3725 2.113860 TGCTGTTAGATGCAGGGTTC 57.886 50.000 0.00 0.00 34.84 3.62
2828 4501 7.486407 AGGACTGGAAATTTTTGCATTAGAT 57.514 32.000 0.00 0.00 37.86 1.98
3325 5448 5.634896 GCAACATTGTCTACTCAGGAAATG 58.365 41.667 0.00 0.00 34.11 2.32
3438 8622 9.959749 TCTTGTTTGGTTTTACATTGATCTTAC 57.040 29.630 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.006772 CACGCGGTAATGAAGAGGC 58.993 57.895 12.47 0.00 0.00 4.70
65 66 0.671781 GAGCCGGCTATGGTATGCTG 60.672 60.000 32.97 0.00 35.50 4.41
106 107 0.183492 ACCATTGTGCGGGATGCTAT 59.817 50.000 0.00 0.00 46.63 2.97
141 142 3.649277 ATGGTCTCTGTCGCGGTGC 62.649 63.158 6.13 0.00 0.00 5.01
151 152 1.685491 GGTACGTGGAGGATGGTCTCT 60.685 57.143 0.00 0.00 34.39 3.10
158 159 0.686769 GGAGTGGGTACGTGGAGGAT 60.687 60.000 0.00 0.00 0.00 3.24
177 178 2.027377 ACAGTCAAAGGGATGAGCTCAG 60.027 50.000 22.96 6.55 0.00 3.35
197 198 0.323451 AGGGCGAAATGGAAGGGAAC 60.323 55.000 0.00 0.00 0.00 3.62
211 212 1.039785 TGAGAGTGATCAGGAGGGCG 61.040 60.000 0.00 0.00 0.00 6.13
215 216 2.093764 GGGTGTTGAGAGTGATCAGGAG 60.094 54.545 0.00 0.00 0.00 3.69
219 220 1.272490 GACGGGTGTTGAGAGTGATCA 59.728 52.381 0.00 0.00 0.00 2.92
221 222 0.608640 GGACGGGTGTTGAGAGTGAT 59.391 55.000 0.00 0.00 0.00 3.06
222 223 0.757561 TGGACGGGTGTTGAGAGTGA 60.758 55.000 0.00 0.00 0.00 3.41
248 249 4.175337 CGGGGGCGTCACATCCAT 62.175 66.667 0.00 0.00 0.00 3.41
266 267 1.134521 AGGAAGCCGCGTTTATCATGA 60.135 47.619 4.92 0.00 0.00 3.07
269 270 1.366111 GCAGGAAGCCGCGTTTATCA 61.366 55.000 4.92 0.00 37.23 2.15
286 287 2.397754 CGTTGCATCGATGGTGGCA 61.398 57.895 26.00 15.22 0.00 4.92
303 304 3.996124 CCCTCTAGCCATCCGCCG 61.996 72.222 0.00 0.00 38.78 6.46
339 340 9.717942 TGGGGAAAAACATTTACATCTAAAATG 57.282 29.630 6.93 6.93 45.59 2.32
342 343 8.251383 TGTGGGGAAAAACATTTACATCTAAA 57.749 30.769 0.00 0.00 0.00 1.85
343 344 7.841282 TGTGGGGAAAAACATTTACATCTAA 57.159 32.000 0.00 0.00 0.00 2.10
344 345 7.841282 TTGTGGGGAAAAACATTTACATCTA 57.159 32.000 0.00 0.00 0.00 1.98
345 346 6.739331 TTGTGGGGAAAAACATTTACATCT 57.261 33.333 0.00 0.00 0.00 2.90
346 347 6.763610 TGTTTGTGGGGAAAAACATTTACATC 59.236 34.615 0.00 0.00 40.41 3.06
347 348 6.653989 TGTTTGTGGGGAAAAACATTTACAT 58.346 32.000 0.00 0.00 40.41 2.29
348 349 6.049955 TGTTTGTGGGGAAAAACATTTACA 57.950 33.333 0.00 0.00 40.41 2.41
354 355 3.107601 TCCATGTTTGTGGGGAAAAACA 58.892 40.909 3.70 3.70 46.90 2.83
355 356 3.118592 TGTCCATGTTTGTGGGGAAAAAC 60.119 43.478 0.00 0.00 39.80 2.43
356 357 3.107601 TGTCCATGTTTGTGGGGAAAAA 58.892 40.909 0.00 0.00 39.80 1.94
357 358 2.752030 TGTCCATGTTTGTGGGGAAAA 58.248 42.857 0.00 0.00 39.80 2.29
358 359 2.461300 TGTCCATGTTTGTGGGGAAA 57.539 45.000 0.00 0.00 39.80 3.13
359 360 2.461300 TTGTCCATGTTTGTGGGGAA 57.539 45.000 0.00 0.00 39.80 3.97
360 361 2.461300 TTTGTCCATGTTTGTGGGGA 57.539 45.000 0.00 0.00 39.80 4.81
363 364 3.248125 GCACAATTTGTCCATGTTTGTGG 59.752 43.478 13.91 0.00 44.48 4.17
364 365 3.060406 CGCACAATTTGTCCATGTTTGTG 60.060 43.478 0.00 9.16 46.13 3.33
365 366 3.122297 CGCACAATTTGTCCATGTTTGT 58.878 40.909 0.00 0.00 0.00 2.83
366 367 3.379240 TCGCACAATTTGTCCATGTTTG 58.621 40.909 0.00 0.00 0.00 2.93
367 368 3.552684 CCTCGCACAATTTGTCCATGTTT 60.553 43.478 0.00 0.00 0.00 2.83
368 369 2.030007 CCTCGCACAATTTGTCCATGTT 60.030 45.455 0.00 0.00 0.00 2.71
369 370 1.541147 CCTCGCACAATTTGTCCATGT 59.459 47.619 0.00 0.00 0.00 3.21
370 371 1.541147 ACCTCGCACAATTTGTCCATG 59.459 47.619 0.00 0.00 0.00 3.66
371 372 1.909700 ACCTCGCACAATTTGTCCAT 58.090 45.000 0.00 0.00 0.00 3.41
372 373 1.686355 AACCTCGCACAATTTGTCCA 58.314 45.000 0.00 0.00 0.00 4.02
373 374 2.393764 CAAACCTCGCACAATTTGTCC 58.606 47.619 0.00 0.00 0.00 4.02
374 375 1.786579 GCAAACCTCGCACAATTTGTC 59.213 47.619 0.00 0.00 35.06 3.18
375 376 1.408702 AGCAAACCTCGCACAATTTGT 59.591 42.857 0.00 0.00 35.06 2.83
376 377 2.138596 AGCAAACCTCGCACAATTTG 57.861 45.000 0.00 0.00 35.57 2.32
377 378 2.888834 AAGCAAACCTCGCACAATTT 57.111 40.000 0.00 0.00 0.00 1.82
378 379 2.888834 AAAGCAAACCTCGCACAATT 57.111 40.000 0.00 0.00 0.00 2.32
379 380 2.100584 TGAAAAGCAAACCTCGCACAAT 59.899 40.909 0.00 0.00 0.00 2.71
380 381 1.474478 TGAAAAGCAAACCTCGCACAA 59.526 42.857 0.00 0.00 0.00 3.33
381 382 1.098869 TGAAAAGCAAACCTCGCACA 58.901 45.000 0.00 0.00 0.00 4.57
382 383 2.202295 TTGAAAAGCAAACCTCGCAC 57.798 45.000 0.00 0.00 32.46 5.34
383 384 2.949451 TTTGAAAAGCAAACCTCGCA 57.051 40.000 0.00 0.00 41.37 5.10
384 385 4.794248 ATTTTTGAAAAGCAAACCTCGC 57.206 36.364 0.00 0.00 45.64 5.03
408 409 9.671279 CCTCCATTTCATAATGTAGTGCATATA 57.329 33.333 0.00 0.00 39.62 0.86
409 410 7.121759 GCCTCCATTTCATAATGTAGTGCATAT 59.878 37.037 0.00 0.00 39.62 1.78
410 411 6.430925 GCCTCCATTTCATAATGTAGTGCATA 59.569 38.462 0.00 0.00 39.62 3.14
411 412 5.242393 GCCTCCATTTCATAATGTAGTGCAT 59.758 40.000 0.00 0.00 39.62 3.96
412 413 4.580167 GCCTCCATTTCATAATGTAGTGCA 59.420 41.667 0.00 0.00 39.62 4.57
413 414 4.580167 TGCCTCCATTTCATAATGTAGTGC 59.420 41.667 0.00 0.00 39.62 4.40
414 415 5.824624 ACTGCCTCCATTTCATAATGTAGTG 59.175 40.000 0.00 0.00 39.62 2.74
415 416 6.006275 ACTGCCTCCATTTCATAATGTAGT 57.994 37.500 0.00 0.00 39.62 2.73
416 417 6.992123 TGTACTGCCTCCATTTCATAATGTAG 59.008 38.462 0.00 0.00 39.62 2.74
417 418 6.765989 GTGTACTGCCTCCATTTCATAATGTA 59.234 38.462 0.00 0.00 39.62 2.29
418 419 5.590259 GTGTACTGCCTCCATTTCATAATGT 59.410 40.000 0.00 0.00 39.62 2.71
419 420 5.589855 TGTGTACTGCCTCCATTTCATAATG 59.410 40.000 0.00 0.00 40.70 1.90
420 421 5.754782 TGTGTACTGCCTCCATTTCATAAT 58.245 37.500 0.00 0.00 0.00 1.28
421 422 5.172687 TGTGTACTGCCTCCATTTCATAA 57.827 39.130 0.00 0.00 0.00 1.90
422 423 4.225042 ACTGTGTACTGCCTCCATTTCATA 59.775 41.667 0.00 0.00 0.00 2.15
423 424 3.009473 ACTGTGTACTGCCTCCATTTCAT 59.991 43.478 0.00 0.00 0.00 2.57
424 425 2.371841 ACTGTGTACTGCCTCCATTTCA 59.628 45.455 0.00 0.00 0.00 2.69
425 426 3.059352 ACTGTGTACTGCCTCCATTTC 57.941 47.619 0.00 0.00 0.00 2.17
426 427 3.583086 ACTACTGTGTACTGCCTCCATTT 59.417 43.478 0.00 0.00 0.00 2.32
427 428 3.173965 ACTACTGTGTACTGCCTCCATT 58.826 45.455 0.00 0.00 0.00 3.16
428 429 2.821437 ACTACTGTGTACTGCCTCCAT 58.179 47.619 0.00 0.00 0.00 3.41
429 430 2.304221 ACTACTGTGTACTGCCTCCA 57.696 50.000 0.00 0.00 0.00 3.86
430 431 4.015084 TCTTACTACTGTGTACTGCCTCC 58.985 47.826 0.00 0.00 0.00 4.30
431 432 5.838531 ATCTTACTACTGTGTACTGCCTC 57.161 43.478 0.00 0.00 0.00 4.70
432 433 6.660800 TCTATCTTACTACTGTGTACTGCCT 58.339 40.000 0.00 0.00 0.00 4.75
433 434 6.939132 TCTATCTTACTACTGTGTACTGCC 57.061 41.667 0.00 0.00 0.00 4.85
434 435 7.799447 CGAATCTATCTTACTACTGTGTACTGC 59.201 40.741 0.00 0.00 0.00 4.40
435 436 8.283992 CCGAATCTATCTTACTACTGTGTACTG 58.716 40.741 0.00 0.00 0.00 2.74
436 437 7.041235 GCCGAATCTATCTTACTACTGTGTACT 60.041 40.741 0.00 0.00 0.00 2.73
437 438 7.076983 GCCGAATCTATCTTACTACTGTGTAC 58.923 42.308 0.00 0.00 0.00 2.90
438 439 6.769341 TGCCGAATCTATCTTACTACTGTGTA 59.231 38.462 0.00 0.00 0.00 2.90
439 440 5.593095 TGCCGAATCTATCTTACTACTGTGT 59.407 40.000 0.00 0.00 0.00 3.72
440 441 6.073327 TGCCGAATCTATCTTACTACTGTG 57.927 41.667 0.00 0.00 0.00 3.66
441 442 6.096423 TGTTGCCGAATCTATCTTACTACTGT 59.904 38.462 0.00 0.00 0.00 3.55
442 443 6.418226 GTGTTGCCGAATCTATCTTACTACTG 59.582 42.308 0.00 0.00 0.00 2.74
443 444 6.505272 GTGTTGCCGAATCTATCTTACTACT 58.495 40.000 0.00 0.00 0.00 2.57
444 445 5.398711 CGTGTTGCCGAATCTATCTTACTAC 59.601 44.000 0.00 0.00 0.00 2.73
445 446 5.066893 ACGTGTTGCCGAATCTATCTTACTA 59.933 40.000 0.00 0.00 0.00 1.82
446 447 4.142227 ACGTGTTGCCGAATCTATCTTACT 60.142 41.667 0.00 0.00 0.00 2.24
447 448 4.110482 ACGTGTTGCCGAATCTATCTTAC 58.890 43.478 0.00 0.00 0.00 2.34
448 449 4.380841 ACGTGTTGCCGAATCTATCTTA 57.619 40.909 0.00 0.00 0.00 2.10
449 450 3.247006 ACGTGTTGCCGAATCTATCTT 57.753 42.857 0.00 0.00 0.00 2.40
450 451 2.961526 ACGTGTTGCCGAATCTATCT 57.038 45.000 0.00 0.00 0.00 1.98
451 452 3.617263 AGAAACGTGTTGCCGAATCTATC 59.383 43.478 0.00 0.00 0.00 2.08
452 453 3.596214 AGAAACGTGTTGCCGAATCTAT 58.404 40.909 0.00 0.00 0.00 1.98
453 454 3.034721 AGAAACGTGTTGCCGAATCTA 57.965 42.857 0.00 0.00 0.00 1.98
454 455 1.878953 AGAAACGTGTTGCCGAATCT 58.121 45.000 0.00 0.00 0.00 2.40
455 456 2.032377 TGAAGAAACGTGTTGCCGAATC 60.032 45.455 0.00 0.00 0.00 2.52
456 457 1.944024 TGAAGAAACGTGTTGCCGAAT 59.056 42.857 0.00 0.00 0.00 3.34
457 458 1.062880 GTGAAGAAACGTGTTGCCGAA 59.937 47.619 0.00 0.00 0.00 4.30
458 459 0.653636 GTGAAGAAACGTGTTGCCGA 59.346 50.000 0.00 0.00 0.00 5.54
459 460 0.375454 TGTGAAGAAACGTGTTGCCG 59.625 50.000 0.00 0.00 0.00 5.69
460 461 2.182014 GTTGTGAAGAAACGTGTTGCC 58.818 47.619 0.00 0.00 0.00 4.52
461 462 2.592459 GTGTTGTGAAGAAACGTGTTGC 59.408 45.455 0.00 0.00 0.00 4.17
462 463 2.837878 CGTGTTGTGAAGAAACGTGTTG 59.162 45.455 0.00 0.00 0.00 3.33
463 464 2.481185 ACGTGTTGTGAAGAAACGTGTT 59.519 40.909 0.00 0.00 44.98 3.32
464 465 2.070783 ACGTGTTGTGAAGAAACGTGT 58.929 42.857 0.00 0.00 44.98 4.49
465 466 2.798834 ACGTGTTGTGAAGAAACGTG 57.201 45.000 0.00 0.00 44.98 4.49
467 468 3.795101 AGTCTACGTGTTGTGAAGAAACG 59.205 43.478 0.00 0.00 40.00 3.60
468 469 5.713822 AAGTCTACGTGTTGTGAAGAAAC 57.286 39.130 0.00 0.00 0.00 2.78
469 470 7.327761 GCTATAAGTCTACGTGTTGTGAAGAAA 59.672 37.037 0.00 0.00 0.00 2.52
470 471 6.805271 GCTATAAGTCTACGTGTTGTGAAGAA 59.195 38.462 0.00 0.00 0.00 2.52
471 472 6.072342 TGCTATAAGTCTACGTGTTGTGAAGA 60.072 38.462 0.00 0.00 0.00 2.87
472 473 6.033619 GTGCTATAAGTCTACGTGTTGTGAAG 59.966 42.308 0.00 0.00 0.00 3.02
473 474 5.860182 GTGCTATAAGTCTACGTGTTGTGAA 59.140 40.000 0.00 0.00 0.00 3.18
474 475 5.048573 TGTGCTATAAGTCTACGTGTTGTGA 60.049 40.000 0.00 0.00 0.00 3.58
475 476 5.158494 TGTGCTATAAGTCTACGTGTTGTG 58.842 41.667 0.00 0.00 0.00 3.33
476 477 5.381174 TGTGCTATAAGTCTACGTGTTGT 57.619 39.130 0.00 0.00 0.00 3.32
477 478 6.887376 AATGTGCTATAAGTCTACGTGTTG 57.113 37.500 0.00 0.00 0.00 3.33
478 479 8.991243 TTTAATGTGCTATAAGTCTACGTGTT 57.009 30.769 0.00 0.00 0.00 3.32
479 480 9.245962 GATTTAATGTGCTATAAGTCTACGTGT 57.754 33.333 0.00 0.00 0.00 4.49
480 481 9.244799 TGATTTAATGTGCTATAAGTCTACGTG 57.755 33.333 0.00 0.00 0.00 4.49
481 482 9.811995 TTGATTTAATGTGCTATAAGTCTACGT 57.188 29.630 0.00 0.00 0.00 3.57
485 486 8.834465 CAGCTTGATTTAATGTGCTATAAGTCT 58.166 33.333 0.00 0.00 0.00 3.24
486 487 8.616076 ACAGCTTGATTTAATGTGCTATAAGTC 58.384 33.333 0.00 0.00 0.00 3.01
487 488 8.400947 CACAGCTTGATTTAATGTGCTATAAGT 58.599 33.333 0.00 0.00 35.35 2.24
488 489 8.400947 ACACAGCTTGATTTAATGTGCTATAAG 58.599 33.333 3.68 0.00 43.92 1.73
489 490 8.279970 ACACAGCTTGATTTAATGTGCTATAA 57.720 30.769 3.68 0.00 43.92 0.98
490 491 7.864108 ACACAGCTTGATTTAATGTGCTATA 57.136 32.000 3.68 0.00 43.92 1.31
491 492 6.764308 ACACAGCTTGATTTAATGTGCTAT 57.236 33.333 3.68 0.00 43.92 2.97
492 493 6.430925 AGAACACAGCTTGATTTAATGTGCTA 59.569 34.615 3.68 0.00 43.92 3.49
493 494 5.242393 AGAACACAGCTTGATTTAATGTGCT 59.758 36.000 3.68 0.00 43.92 4.40
494 495 5.464168 AGAACACAGCTTGATTTAATGTGC 58.536 37.500 3.68 0.00 43.92 4.57
501 502 9.453572 TTGAGATAATAGAACACAGCTTGATTT 57.546 29.630 3.37 0.00 0.00 2.17
502 503 9.453572 TTTGAGATAATAGAACACAGCTTGATT 57.546 29.630 3.37 0.00 0.00 2.57
503 504 8.887717 GTTTGAGATAATAGAACACAGCTTGAT 58.112 33.333 3.37 0.00 0.00 2.57
504 505 7.877612 TGTTTGAGATAATAGAACACAGCTTGA 59.122 33.333 3.37 0.00 0.00 3.02
505 506 8.032952 TGTTTGAGATAATAGAACACAGCTTG 57.967 34.615 0.00 0.00 0.00 4.01
506 507 8.621532 TTGTTTGAGATAATAGAACACAGCTT 57.378 30.769 0.00 0.00 30.71 3.74
507 508 8.507249 GTTTGTTTGAGATAATAGAACACAGCT 58.493 33.333 0.00 0.00 30.71 4.24
508 509 8.507249 AGTTTGTTTGAGATAATAGAACACAGC 58.493 33.333 0.00 0.00 30.71 4.40
510 511 8.708742 CGAGTTTGTTTGAGATAATAGAACACA 58.291 33.333 0.00 0.00 30.71 3.72
511 512 8.709646 ACGAGTTTGTTTGAGATAATAGAACAC 58.290 33.333 0.00 0.00 30.71 3.32
512 513 8.827177 ACGAGTTTGTTTGAGATAATAGAACA 57.173 30.769 0.00 0.00 0.00 3.18
513 514 8.102716 CGACGAGTTTGTTTGAGATAATAGAAC 58.897 37.037 0.00 0.00 0.00 3.01
514 515 8.024865 TCGACGAGTTTGTTTGAGATAATAGAA 58.975 33.333 0.00 0.00 0.00 2.10
515 516 7.484007 GTCGACGAGTTTGTTTGAGATAATAGA 59.516 37.037 0.00 0.00 0.00 1.98
516 517 7.272731 TGTCGACGAGTTTGTTTGAGATAATAG 59.727 37.037 11.62 0.00 0.00 1.73
517 518 7.061441 GTGTCGACGAGTTTGTTTGAGATAATA 59.939 37.037 11.62 0.00 0.00 0.98
518 519 5.924254 TGTCGACGAGTTTGTTTGAGATAAT 59.076 36.000 11.62 0.00 0.00 1.28
519 520 5.174398 GTGTCGACGAGTTTGTTTGAGATAA 59.826 40.000 11.62 0.00 0.00 1.75
520 521 4.678287 GTGTCGACGAGTTTGTTTGAGATA 59.322 41.667 11.62 0.00 0.00 1.98
521 522 3.489785 GTGTCGACGAGTTTGTTTGAGAT 59.510 43.478 11.62 0.00 0.00 2.75
522 523 2.855963 GTGTCGACGAGTTTGTTTGAGA 59.144 45.455 11.62 0.00 0.00 3.27
523 524 2.034001 GGTGTCGACGAGTTTGTTTGAG 60.034 50.000 11.62 0.00 0.00 3.02
524 525 1.928503 GGTGTCGACGAGTTTGTTTGA 59.071 47.619 11.62 0.00 0.00 2.69
525 526 1.931172 AGGTGTCGACGAGTTTGTTTG 59.069 47.619 11.62 0.00 0.00 2.93
526 527 2.304751 AGGTGTCGACGAGTTTGTTT 57.695 45.000 11.62 0.00 0.00 2.83
527 528 2.199236 GAAGGTGTCGACGAGTTTGTT 58.801 47.619 11.62 0.00 0.00 2.83
528 529 1.135527 TGAAGGTGTCGACGAGTTTGT 59.864 47.619 11.62 0.00 0.00 2.83
529 530 1.847818 TGAAGGTGTCGACGAGTTTG 58.152 50.000 11.62 0.00 0.00 2.93
530 531 2.296471 AGATGAAGGTGTCGACGAGTTT 59.704 45.455 11.62 2.62 0.00 2.66
531 532 1.887198 AGATGAAGGTGTCGACGAGTT 59.113 47.619 11.62 3.34 0.00 3.01
532 533 1.469308 GAGATGAAGGTGTCGACGAGT 59.531 52.381 11.62 0.00 0.00 4.18
533 534 1.740585 AGAGATGAAGGTGTCGACGAG 59.259 52.381 11.62 0.00 0.00 4.18
534 535 1.822506 AGAGATGAAGGTGTCGACGA 58.177 50.000 11.62 0.00 0.00 4.20
535 536 2.678836 AGTAGAGATGAAGGTGTCGACG 59.321 50.000 11.62 0.00 0.00 5.12
536 537 3.065648 GGAGTAGAGATGAAGGTGTCGAC 59.934 52.174 9.11 9.11 0.00 4.20
537 538 3.054287 AGGAGTAGAGATGAAGGTGTCGA 60.054 47.826 0.00 0.00 0.00 4.20
538 539 3.283751 AGGAGTAGAGATGAAGGTGTCG 58.716 50.000 0.00 0.00 0.00 4.35
539 540 6.322712 ACATTAGGAGTAGAGATGAAGGTGTC 59.677 42.308 0.00 0.00 0.00 3.67
540 541 6.198639 ACATTAGGAGTAGAGATGAAGGTGT 58.801 40.000 0.00 0.00 0.00 4.16
541 542 6.549364 AGACATTAGGAGTAGAGATGAAGGTG 59.451 42.308 0.00 0.00 0.00 4.00
542 543 6.678547 AGACATTAGGAGTAGAGATGAAGGT 58.321 40.000 0.00 0.00 0.00 3.50
543 544 6.775142 TGAGACATTAGGAGTAGAGATGAAGG 59.225 42.308 0.00 0.00 0.00 3.46
544 545 7.502226 ACTGAGACATTAGGAGTAGAGATGAAG 59.498 40.741 0.00 0.00 0.00 3.02
545 546 7.350382 ACTGAGACATTAGGAGTAGAGATGAA 58.650 38.462 0.00 0.00 0.00 2.57
546 547 6.905736 ACTGAGACATTAGGAGTAGAGATGA 58.094 40.000 0.00 0.00 0.00 2.92
547 548 7.424803 CAACTGAGACATTAGGAGTAGAGATG 58.575 42.308 0.00 0.00 0.00 2.90
756 758 8.868635 TGGTTAATTTTCGTCGGTTAATTTTT 57.131 26.923 0.00 0.00 0.00 1.94
877 894 0.394488 ACGAGGGCAGAGATTCGAGA 60.394 55.000 0.00 0.00 36.89 4.04
878 895 0.457851 AACGAGGGCAGAGATTCGAG 59.542 55.000 0.00 0.00 36.89 4.04
879 896 0.456221 GAACGAGGGCAGAGATTCGA 59.544 55.000 0.00 0.00 36.89 3.71
880 897 0.867753 CGAACGAGGGCAGAGATTCG 60.868 60.000 0.00 0.00 38.88 3.34
881 898 1.148759 GCGAACGAGGGCAGAGATTC 61.149 60.000 0.00 0.00 0.00 2.52
882 899 1.153549 GCGAACGAGGGCAGAGATT 60.154 57.895 0.00 0.00 0.00 2.40
883 900 2.496817 GCGAACGAGGGCAGAGAT 59.503 61.111 0.00 0.00 0.00 2.75
1201 1259 1.456705 GACTCCGCTCCTCCTCCAT 60.457 63.158 0.00 0.00 0.00 3.41
1241 1299 2.037367 TGAGCGCCTACCTGGAGT 59.963 61.111 2.29 0.00 37.96 3.85
1331 1389 3.680786 CCGAGCACGACCTGGTCA 61.681 66.667 25.42 0.00 46.22 4.02
1359 1417 3.562973 GCATTCAACCACGAGATCATGAT 59.437 43.478 8.25 8.25 0.00 2.45
1602 2308 2.031769 TGCGTCAACTGAAGAATTGCAG 60.032 45.455 0.00 0.00 38.10 4.41
1629 2335 7.648908 CACAATGTAGAAAACTGATGCTTTTGA 59.351 33.333 0.00 0.00 0.00 2.69
1716 2422 3.117701 TCAATGGTGGAGAACAACCTGAA 60.118 43.478 0.00 0.00 35.29 3.02
2155 3214 4.348863 AGAAAGTGTGTCTGATTGCTCT 57.651 40.909 0.00 0.00 0.00 4.09
2369 3543 5.128827 TGTGGATCTTATGTACCTTGAGGAC 59.871 44.000 3.59 0.00 38.94 3.85
2475 3649 4.853924 AGGCAGGACAAAGTAACAATTG 57.146 40.909 3.24 3.24 0.00 2.32
2547 3725 3.822735 ACACTGGTCAAAAGTGATCATGG 59.177 43.478 10.35 0.00 44.00 3.66
2702 4262 5.758296 TCACTTACCTGAGATGTGTTTTGTC 59.242 40.000 0.00 0.00 0.00 3.18
2703 4263 5.680619 TCACTTACCTGAGATGTGTTTTGT 58.319 37.500 0.00 0.00 0.00 2.83
2704 4264 5.334414 GCTCACTTACCTGAGATGTGTTTTG 60.334 44.000 0.27 0.00 40.28 2.44
3353 5476 2.540383 AGGGTACTCTGCATCAGTTCA 58.460 47.619 0.00 0.00 32.61 3.18
3438 8622 1.938016 GCCCAAAAACTGAGCATGCAG 60.938 52.381 21.98 12.16 41.63 4.41


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

AutoCloner maintained by Alex Coulton.