Multiple sequence alignment - TraesCS4A01G312500

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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 TraesCS4A01G312500 chr4A 100.000 2780 0 0 1 2780 603636540 603633761 0.000000e+00 5134
1 TraesCS4A01G312500 chr4D 87.194 1593 109 40 469 2016 1205309 1206851 0.000000e+00 1724
2 TraesCS4A01G312500 chr4D 87.452 263 20 5 165 427 129038458 129038707 9.740000e-75 291
3 TraesCS4A01G312500 chr4D 76.101 636 95 39 2191 2780 52067273 52066649 2.110000e-71 279
4 TraesCS4A01G312500 chr6A 83.651 1835 170 63 357 2131 27764749 27766513 0.000000e+00 1607
5 TraesCS4A01G312500 chr6A 85.507 276 35 5 2150 2423 135242871 135242599 1.630000e-72 283
6 TraesCS4A01G312500 chrUn 84.061 1719 165 51 357 2016 112252396 112254064 0.000000e+00 1555
7 TraesCS4A01G312500 chrUn 87.452 263 19 6 165 427 440736941 440736693 9.740000e-75 291
8 TraesCS4A01G312500 chrUn 87.452 263 20 5 165 427 446119204 446119453 9.740000e-75 291
9 TraesCS4A01G312500 chrUn 87.072 263 21 5 165 427 249264452 249264701 4.530000e-73 285
10 TraesCS4A01G312500 chr6B 84.681 1534 130 52 357 1832 48544601 48546087 0.000000e+00 1434
11 TraesCS4A01G312500 chr4B 90.705 667 48 8 630 1294 806334 805680 0.000000e+00 876
12 TraesCS4A01G312500 chr4B 83.784 629 63 15 1397 2016 672108 671510 6.720000e-156 560
13 TraesCS4A01G312500 chr4B 87.738 473 33 9 1331 1784 805675 805209 1.900000e-146 529
14 TraesCS4A01G312500 chr4B 93.043 115 7 1 489 603 806445 806332 1.710000e-37 167
15 TraesCS4A01G312500 chr4B 83.019 159 17 6 1796 1950 805088 804936 4.830000e-28 135
16 TraesCS4A01G312500 chr4B 95.238 63 2 1 48 110 806972 806911 6.340000e-17 99
17 TraesCS4A01G312500 chr2D 85.778 675 52 23 2146 2780 380580747 380581417 0.000000e+00 675
18 TraesCS4A01G312500 chr2D 85.455 275 36 4 2150 2423 441032293 441032564 1.630000e-72 283
19 TraesCS4A01G312500 chr2D 85.145 276 38 3 2150 2423 142672206 142672480 2.110000e-71 279
20 TraesCS4A01G312500 chr2A 83.976 674 68 13 2146 2780 751997420 751996748 6.580000e-171 610
21 TraesCS4A01G312500 chr2A 86.631 374 31 9 2424 2780 748986784 748987155 2.010000e-106 396
22 TraesCS4A01G312500 chr2A 83.914 373 31 11 2423 2780 356676697 356677055 2.060000e-86 329
23 TraesCS4A01G312500 chr2A 85.252 278 39 2 2148 2423 15090888 15091165 4.530000e-73 285
24 TraesCS4A01G312500 chr3D 82.517 572 55 24 2147 2688 86361205 86361761 7.020000e-126 460
25 TraesCS4A01G312500 chr3D 85.027 374 34 8 2423 2778 589879729 589879360 7.320000e-96 361
26 TraesCS4A01G312500 chr3D 87.452 263 20 5 165 427 351694795 351695044 9.740000e-75 291
27 TraesCS4A01G312500 chr3D 87.072 263 21 5 165 427 198268340 198268589 4.530000e-73 285
28 TraesCS4A01G312500 chr6D 86.631 374 31 6 2423 2780 438098414 438098044 2.010000e-106 396
29 TraesCS4A01G312500 chr6D 83.333 378 38 11 2423 2780 402887938 402888310 2.670000e-85 326
30 TraesCS4A01G312500 chr6D 87.452 263 20 5 165 427 51098813 51099062 9.740000e-75 291
31 TraesCS4A01G312500 chr6D 85.000 220 10 11 2423 2623 427753648 427753863 4.690000e-48 202
32 TraesCS4A01G312500 chr7D 86.400 375 32 8 2423 2780 575592052 575591680 2.600000e-105 392
33 TraesCS4A01G312500 chr7D 86.908 359 22 15 486 843 412486000 412486334 2.020000e-101 379
34 TraesCS4A01G312500 chr7D 89.209 278 29 1 2147 2423 575592375 575592098 2.050000e-91 346
35 TraesCS4A01G312500 chr7D 87.452 263 20 5 165 427 399497860 399497611 9.740000e-75 291
36 TraesCS4A01G312500 chr7D 87.072 263 21 5 165 427 408599931 408600180 4.530000e-73 285
37 TraesCS4A01G312500 chr7D 95.588 68 2 1 48 115 412485652 412485718 1.050000e-19 108
38 TraesCS4A01G312500 chr5D 86.523 371 29 8 2423 2775 396285181 396285548 3.360000e-104 388
39 TraesCS4A01G312500 chr3A 85.867 375 34 6 2423 2780 182616926 182616554 5.620000e-102 381
40 TraesCS4A01G312500 chr1D 84.656 378 31 11 2423 2780 254690745 254691115 4.410000e-93 351
41 TraesCS4A01G312500 chr1D 87.097 279 33 3 2147 2423 254690422 254690699 2.080000e-81 313
42 TraesCS4A01G312500 chr1D 84.532 278 35 8 2150 2423 320210993 320210720 4.560000e-68 268
43 TraesCS4A01G312500 chr1D 83.108 296 40 9 2134 2423 287672551 287672260 7.640000e-66 261
44 TraesCS4A01G312500 chr1A 84.409 372 37 11 2423 2780 230614588 230614224 2.050000e-91 346
45 TraesCS4A01G312500 chr5A 84.643 280 37 5 2147 2423 502183745 502183469 9.810000e-70 274
46 TraesCS4A01G312500 chr3B 78.378 370 57 20 2420 2780 226784068 226784423 4.660000e-53 219


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 TraesCS4A01G312500 chr4A 603633761 603636540 2779 True 5134.0 5134 100.0000 1 2780 1 chr4A.!!$R1 2779
1 TraesCS4A01G312500 chr4D 1205309 1206851 1542 False 1724.0 1724 87.1940 469 2016 1 chr4D.!!$F1 1547
2 TraesCS4A01G312500 chr4D 52066649 52067273 624 True 279.0 279 76.1010 2191 2780 1 chr4D.!!$R1 589
3 TraesCS4A01G312500 chr6A 27764749 27766513 1764 False 1607.0 1607 83.6510 357 2131 1 chr6A.!!$F1 1774
4 TraesCS4A01G312500 chrUn 112252396 112254064 1668 False 1555.0 1555 84.0610 357 2016 1 chrUn.!!$F1 1659
5 TraesCS4A01G312500 chr6B 48544601 48546087 1486 False 1434.0 1434 84.6810 357 1832 1 chr6B.!!$F1 1475
6 TraesCS4A01G312500 chr4B 671510 672108 598 True 560.0 560 83.7840 1397 2016 1 chr4B.!!$R1 619
7 TraesCS4A01G312500 chr4B 804936 806972 2036 True 361.2 876 89.9486 48 1950 5 chr4B.!!$R2 1902
8 TraesCS4A01G312500 chr2D 380580747 380581417 670 False 675.0 675 85.7780 2146 2780 1 chr2D.!!$F2 634
9 TraesCS4A01G312500 chr2A 751996748 751997420 672 True 610.0 610 83.9760 2146 2780 1 chr2A.!!$R1 634
10 TraesCS4A01G312500 chr3D 86361205 86361761 556 False 460.0 460 82.5170 2147 2688 1 chr3D.!!$F1 541
11 TraesCS4A01G312500 chr7D 575591680 575592375 695 True 369.0 392 87.8045 2147 2780 2 chr7D.!!$R2 633
12 TraesCS4A01G312500 chr7D 412485652 412486334 682 False 243.5 379 91.2480 48 843 2 chr7D.!!$F2 795
13 TraesCS4A01G312500 chr1D 254690422 254691115 693 False 332.0 351 85.8765 2147 2780 2 chr1D.!!$F1 633

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
327 612 0.760945 AGCTAGAAGGGCATACGGCT 60.761 55.0 0.0 0.0 44.01 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2584 0.106819 CTAAATGCCTGGCTCTGGCT 60.107 55.0 21.03 1.14 46.43 4.75 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
27 28 7.959689 CATACATAATGTTCTCTTCTCCTGG 57.040 40.000 0.00 0.00 0.00 4.45
28 29 5.365021 ACATAATGTTCTCTTCTCCTGGG 57.635 43.478 0.00 0.00 0.00 4.45
29 30 5.032846 ACATAATGTTCTCTTCTCCTGGGA 58.967 41.667 0.00 0.00 0.00 4.37
30 31 5.488919 ACATAATGTTCTCTTCTCCTGGGAA 59.511 40.000 0.00 0.00 0.00 3.97
31 32 4.566426 AATGTTCTCTTCTCCTGGGAAG 57.434 45.455 14.96 14.96 42.72 3.46
32 33 3.260269 TGTTCTCTTCTCCTGGGAAGA 57.740 47.619 19.73 19.73 46.22 2.87
33 34 3.796111 TGTTCTCTTCTCCTGGGAAGAT 58.204 45.455 20.63 0.00 46.84 2.40
34 35 3.517100 TGTTCTCTTCTCCTGGGAAGATG 59.483 47.826 20.63 16.14 46.84 2.90
35 36 3.765432 TCTCTTCTCCTGGGAAGATGA 57.235 47.619 20.63 17.43 46.84 2.92
36 37 3.370104 TCTCTTCTCCTGGGAAGATGAC 58.630 50.000 20.63 0.00 46.84 3.06
37 38 3.012274 TCTCTTCTCCTGGGAAGATGACT 59.988 47.826 20.63 0.00 46.84 3.41
38 39 4.230733 TCTCTTCTCCTGGGAAGATGACTA 59.769 45.833 20.63 8.08 46.84 2.59
39 40 4.947883 TCTTCTCCTGGGAAGATGACTAA 58.052 43.478 18.05 1.78 44.37 2.24
40 41 4.959210 TCTTCTCCTGGGAAGATGACTAAG 59.041 45.833 18.05 0.34 44.37 2.18
41 42 4.338795 TCTCCTGGGAAGATGACTAAGT 57.661 45.455 0.00 0.00 0.00 2.24
42 43 4.026744 TCTCCTGGGAAGATGACTAAGTG 58.973 47.826 0.00 0.00 0.00 3.16
43 44 2.501723 TCCTGGGAAGATGACTAAGTGC 59.498 50.000 0.00 0.00 0.00 4.40
44 45 2.237143 CCTGGGAAGATGACTAAGTGCA 59.763 50.000 0.00 0.00 0.00 4.57
45 46 3.529533 CTGGGAAGATGACTAAGTGCAG 58.470 50.000 0.00 0.00 0.00 4.41
46 47 3.173151 TGGGAAGATGACTAAGTGCAGA 58.827 45.455 0.00 0.00 0.00 4.26
115 116 2.711542 GGGGTGATCAACTGTGGTTAG 58.288 52.381 11.29 0.00 33.88 2.34
140 175 9.452287 AGCCAAAAATAATGAAACTTGCATAAT 57.548 25.926 0.00 0.00 0.00 1.28
142 177 9.493206 CCAAAAATAATGAAACTTGCATAATGC 57.507 29.630 0.00 0.00 45.29 3.56
217 502 8.458052 ACGCTTGATATACACAAAAATGATGAA 58.542 29.630 0.00 0.00 0.00 2.57
257 542 2.509964 AGACAACCCCCTAGCTAAATGG 59.490 50.000 0.00 0.00 0.00 3.16
303 588 5.913137 TCAAGCAGAAAAACAGAGGAAAA 57.087 34.783 0.00 0.00 0.00 2.29
304 589 5.894807 TCAAGCAGAAAAACAGAGGAAAAG 58.105 37.500 0.00 0.00 0.00 2.27
305 590 4.313277 AGCAGAAAAACAGAGGAAAAGC 57.687 40.909 0.00 0.00 0.00 3.51
306 591 3.701040 AGCAGAAAAACAGAGGAAAAGCA 59.299 39.130 0.00 0.00 0.00 3.91
307 592 4.343239 AGCAGAAAAACAGAGGAAAAGCAT 59.657 37.500 0.00 0.00 0.00 3.79
308 593 5.536161 AGCAGAAAAACAGAGGAAAAGCATA 59.464 36.000 0.00 0.00 0.00 3.14
309 594 5.860716 GCAGAAAAACAGAGGAAAAGCATAG 59.139 40.000 0.00 0.00 0.00 2.23
310 595 5.860716 CAGAAAAACAGAGGAAAAGCATAGC 59.139 40.000 0.00 0.00 0.00 2.97
311 596 5.772169 AGAAAAACAGAGGAAAAGCATAGCT 59.228 36.000 0.00 0.00 42.56 3.32
312 597 6.942576 AGAAAAACAGAGGAAAAGCATAGCTA 59.057 34.615 0.00 0.00 38.25 3.32
313 598 6.749923 AAAACAGAGGAAAAGCATAGCTAG 57.250 37.500 0.00 0.00 38.25 3.42
314 599 5.683876 AACAGAGGAAAAGCATAGCTAGA 57.316 39.130 0.00 0.00 38.25 2.43
315 600 5.683876 ACAGAGGAAAAGCATAGCTAGAA 57.316 39.130 0.00 0.00 38.25 2.10
316 601 5.669477 ACAGAGGAAAAGCATAGCTAGAAG 58.331 41.667 0.00 0.00 38.25 2.85
317 602 5.055812 CAGAGGAAAAGCATAGCTAGAAGG 58.944 45.833 0.00 0.00 38.25 3.46
318 603 4.102367 AGAGGAAAAGCATAGCTAGAAGGG 59.898 45.833 0.00 0.00 38.25 3.95
319 604 2.881513 GGAAAAGCATAGCTAGAAGGGC 59.118 50.000 0.00 0.00 38.25 5.19
320 605 3.545703 GAAAAGCATAGCTAGAAGGGCA 58.454 45.455 0.00 0.00 38.25 5.36
321 606 3.872459 AAAGCATAGCTAGAAGGGCAT 57.128 42.857 0.00 0.00 38.25 4.40
322 607 4.982241 AAAGCATAGCTAGAAGGGCATA 57.018 40.909 0.00 0.00 38.25 3.14
323 608 3.971245 AGCATAGCTAGAAGGGCATAC 57.029 47.619 0.00 0.00 36.99 2.39
324 609 2.232452 AGCATAGCTAGAAGGGCATACG 59.768 50.000 0.00 0.00 36.99 3.06
325 610 2.675317 GCATAGCTAGAAGGGCATACGG 60.675 54.545 0.00 0.00 0.00 4.02
326 611 0.966920 TAGCTAGAAGGGCATACGGC 59.033 55.000 0.00 0.00 43.74 5.68
327 612 0.760945 AGCTAGAAGGGCATACGGCT 60.761 55.000 0.00 0.00 44.01 5.52
328 613 0.966920 GCTAGAAGGGCATACGGCTA 59.033 55.000 0.00 0.00 44.01 3.93
329 614 1.343465 GCTAGAAGGGCATACGGCTAA 59.657 52.381 0.00 0.00 44.01 3.09
330 615 2.028020 GCTAGAAGGGCATACGGCTAAT 60.028 50.000 0.00 0.00 44.01 1.73
331 616 3.194968 GCTAGAAGGGCATACGGCTAATA 59.805 47.826 0.00 0.00 44.01 0.98
332 617 3.963428 AGAAGGGCATACGGCTAATAG 57.037 47.619 0.00 0.00 44.01 1.73
333 618 3.240302 AGAAGGGCATACGGCTAATAGT 58.760 45.455 0.00 0.00 44.01 2.12
334 619 3.006967 AGAAGGGCATACGGCTAATAGTG 59.993 47.826 0.00 0.00 44.01 2.74
335 620 1.623811 AGGGCATACGGCTAATAGTGG 59.376 52.381 0.00 0.00 44.01 4.00
336 621 1.346722 GGGCATACGGCTAATAGTGGT 59.653 52.381 0.00 0.00 44.01 4.16
337 622 2.564062 GGGCATACGGCTAATAGTGGTA 59.436 50.000 0.00 0.00 44.01 3.25
338 623 3.197116 GGGCATACGGCTAATAGTGGTAT 59.803 47.826 0.00 0.00 44.01 2.73
339 624 4.403432 GGGCATACGGCTAATAGTGGTATA 59.597 45.833 5.50 0.00 44.01 1.47
340 625 5.070047 GGGCATACGGCTAATAGTGGTATAT 59.930 44.000 5.50 0.00 44.01 0.86
341 626 6.266103 GGGCATACGGCTAATAGTGGTATATA 59.734 42.308 5.50 0.00 44.01 0.86
342 627 7.039223 GGGCATACGGCTAATAGTGGTATATAT 60.039 40.741 5.50 0.00 44.01 0.86
343 628 9.017509 GGCATACGGCTAATAGTGGTATATATA 57.982 37.037 5.50 0.00 44.01 0.86
347 632 8.461249 ACGGCTAATAGTGGTATATATAGGTG 57.539 38.462 0.00 0.00 0.00 4.00
348 633 7.014038 ACGGCTAATAGTGGTATATATAGGTGC 59.986 40.741 0.00 0.00 0.00 5.01
349 634 7.230913 CGGCTAATAGTGGTATATATAGGTGCT 59.769 40.741 0.00 0.00 0.00 4.40
350 635 9.584008 GGCTAATAGTGGTATATATAGGTGCTA 57.416 37.037 0.00 0.00 0.00 3.49
353 638 8.480133 AATAGTGGTATATATAGGTGCTAGGC 57.520 38.462 0.00 0.00 0.00 3.93
354 639 5.838955 AGTGGTATATATAGGTGCTAGGCA 58.161 41.667 0.00 0.00 35.60 4.75
355 640 5.894393 AGTGGTATATATAGGTGCTAGGCAG 59.106 44.000 0.00 0.00 40.08 4.85
365 650 2.764572 GGTGCTAGGCAGTAGGTTCTTA 59.235 50.000 0.00 0.00 40.08 2.10
391 676 3.823304 AGAGTAGTATGCGCATCATCAGA 59.177 43.478 29.11 4.90 36.63 3.27
393 678 3.823304 AGTAGTATGCGCATCATCAGAGA 59.177 43.478 29.11 3.10 36.63 3.10
412 697 9.775854 ATCAGAGATTTGACACATAGGATTAAG 57.224 33.333 0.00 0.00 0.00 1.85
417 702 9.388506 AGATTTGACACATAGGATTAAGTGAAG 57.611 33.333 0.00 0.00 33.75 3.02
418 703 9.167311 GATTTGACACATAGGATTAAGTGAAGT 57.833 33.333 0.00 0.00 33.75 3.01
476 779 7.559335 TGGGCTTGAGAATGAGTACATATAT 57.441 36.000 0.00 0.00 35.50 0.86
529 832 2.678336 GTTCATTCTACCAGCTTTCCCG 59.322 50.000 0.00 0.00 0.00 5.14
600 903 6.209391 CCTGAAGTTATGACATTTTGTTCCCT 59.791 38.462 0.00 0.00 0.00 4.20
633 952 5.107220 GGTACTAAGTTTGTCGGACATGTTG 60.107 44.000 12.26 0.00 0.00 3.33
648 967 6.533367 CGGACATGTTGAAAAGAAAGGAAAAA 59.467 34.615 0.00 0.00 0.00 1.94
716 1037 4.796038 AGATCCCTCAAGCAAACAAATG 57.204 40.909 0.00 0.00 0.00 2.32
719 1040 1.693606 CCCTCAAGCAAACAAATGGGT 59.306 47.619 0.00 0.00 0.00 4.51
721 1042 3.132925 CCTCAAGCAAACAAATGGGTTG 58.867 45.455 0.00 0.00 43.43 3.77
761 1088 6.328148 TCCTTTGTCACTTTAGTCCCTTTCTA 59.672 38.462 0.00 0.00 0.00 2.10
814 1141 4.270317 ACCAGGCTTTTGGATAATGGAT 57.730 40.909 9.00 0.00 40.87 3.41
815 1142 5.402054 ACCAGGCTTTTGGATAATGGATA 57.598 39.130 9.00 0.00 40.87 2.59
816 1143 5.776358 ACCAGGCTTTTGGATAATGGATAA 58.224 37.500 9.00 0.00 40.87 1.75
818 1145 6.494835 ACCAGGCTTTTGGATAATGGATAATC 59.505 38.462 9.00 0.00 40.87 1.75
819 1146 6.494491 CCAGGCTTTTGGATAATGGATAATCA 59.506 38.462 0.00 0.00 40.87 2.57
820 1147 7.015487 CCAGGCTTTTGGATAATGGATAATCAA 59.985 37.037 0.00 0.00 40.87 2.57
821 1148 8.423349 CAGGCTTTTGGATAATGGATAATCAAA 58.577 33.333 0.00 0.00 0.00 2.69
822 1149 9.162733 AGGCTTTTGGATAATGGATAATCAAAT 57.837 29.630 0.00 0.00 0.00 2.32
823 1150 9.783081 GGCTTTTGGATAATGGATAATCAAATT 57.217 29.630 0.00 0.00 0.00 1.82
863 1194 6.299141 AGACCGTGCCTGATTAATTATTCAT 58.701 36.000 9.81 0.00 0.00 2.57
880 1212 3.806949 TCATCAAACCAAGCTAACCCT 57.193 42.857 0.00 0.00 0.00 4.34
1042 1374 1.444895 GGCGCATGCAAGTTCCTTG 60.445 57.895 19.57 0.00 45.35 3.61
1071 1403 0.238289 GCGTCAATGGGTGTGTCTTG 59.762 55.000 0.00 0.00 0.00 3.02
1074 1406 0.478072 TCAATGGGTGTGTCTTGGCT 59.522 50.000 0.00 0.00 0.00 4.75
1083 1415 0.947244 GTGTCTTGGCTCCACACTTG 59.053 55.000 6.27 0.00 37.93 3.16
1089 1421 2.555547 GGCTCCACACTTGTGCCAC 61.556 63.158 3.68 0.00 44.34 5.01
1149 1481 4.389576 GGTGCAAGCAACGCCTCG 62.390 66.667 0.00 0.00 34.75 4.63
1290 1622 2.612972 GCAGCAGCAGGTTAGTGAGTTA 60.613 50.000 0.00 0.00 41.58 2.24
1328 1668 6.485313 ACCGACTTGAACAACAATTCTATTGA 59.515 34.615 6.42 0.00 36.47 2.57
1500 1860 3.902881 AGCCCTGAAGAAGACAGTATG 57.097 47.619 0.00 0.00 46.00 2.39
1506 1866 4.323028 CCTGAAGAAGACAGTATGAAGGCA 60.323 45.833 0.00 0.00 39.69 4.75
1662 2034 4.242475 ACAGTTCACATGTATACACACCG 58.758 43.478 7.96 0.00 37.54 4.94
1677 2049 0.311165 CACCGGACTATACAGCCTCG 59.689 60.000 9.46 0.00 0.00 4.63
1678 2050 0.106819 ACCGGACTATACAGCCTCGT 60.107 55.000 9.46 0.00 0.00 4.18
1679 2051 1.030457 CCGGACTATACAGCCTCGTT 58.970 55.000 0.00 0.00 0.00 3.85
1680 2052 1.407979 CCGGACTATACAGCCTCGTTT 59.592 52.381 0.00 0.00 0.00 3.60
1681 2053 2.620115 CCGGACTATACAGCCTCGTTTA 59.380 50.000 0.00 0.00 0.00 2.01
1682 2054 3.067180 CCGGACTATACAGCCTCGTTTAA 59.933 47.826 0.00 0.00 0.00 1.52
1737 2109 3.438781 TGTTTCCCGTTGATATGCAAGAC 59.561 43.478 0.00 0.00 37.12 3.01
1767 2140 5.239525 GCAAGAGAATGGGTATTATGACACC 59.760 44.000 0.00 0.00 0.00 4.16
1828 2318 3.311106 CATGTGCTTGGTAACTGCAAAG 58.689 45.455 0.86 0.00 45.16 2.77
1925 2432 6.434028 AGCCTGTACTAAAATGCTGAATCAAA 59.566 34.615 0.00 0.00 0.00 2.69
1950 2457 7.231467 ACAGGGTGTAGAAGACATATGTTTTT 58.769 34.615 10.30 7.95 41.14 1.94
1976 2483 6.985188 TTTACTAACCATCAGTGATGAAGC 57.015 37.500 30.63 0.00 42.09 3.86
1996 2503 2.117137 CATGCTGAAATGCTTCATCGC 58.883 47.619 0.00 0.00 40.78 4.58
2023 2530 6.653273 TTTTTCGCTCTAGTGAATCATGAG 57.347 37.500 6.79 6.54 43.15 2.90
2024 2531 5.582689 TTTCGCTCTAGTGAATCATGAGA 57.417 39.130 6.79 6.13 43.15 3.27
2025 2532 4.827304 TCGCTCTAGTGAATCATGAGAG 57.173 45.455 15.78 15.78 37.34 3.20
2026 2533 4.455606 TCGCTCTAGTGAATCATGAGAGA 58.544 43.478 21.30 16.02 36.55 3.10
2027 2534 5.069318 TCGCTCTAGTGAATCATGAGAGAT 58.931 41.667 21.30 0.00 36.55 2.75
2028 2535 6.234177 TCGCTCTAGTGAATCATGAGAGATA 58.766 40.000 21.30 10.02 36.55 1.98
2029 2536 6.148645 TCGCTCTAGTGAATCATGAGAGATAC 59.851 42.308 21.30 8.51 36.55 2.24
2030 2537 6.149308 CGCTCTAGTGAATCATGAGAGATACT 59.851 42.308 21.30 4.11 36.55 2.12
2031 2538 7.307694 GCTCTAGTGAATCATGAGAGATACTG 58.692 42.308 21.30 3.06 36.55 2.74
2032 2539 7.174772 GCTCTAGTGAATCATGAGAGATACTGA 59.825 40.741 21.30 2.35 36.55 3.41
2033 2540 9.234827 CTCTAGTGAATCATGAGAGATACTGAT 57.765 37.037 15.28 0.00 36.55 2.90
2042 2549 6.723052 TCATGAGAGATACTGATATGCCAAGA 59.277 38.462 0.00 0.00 0.00 3.02
2046 2553 8.693625 TGAGAGATACTGATATGCCAAGATATG 58.306 37.037 0.00 0.00 0.00 1.78
2058 2565 4.949856 TGCCAAGATATGTTTTTCTCTCCC 59.050 41.667 0.00 0.00 0.00 4.30
2059 2566 4.339530 GCCAAGATATGTTTTTCTCTCCCC 59.660 45.833 0.00 0.00 0.00 4.81
2071 2578 7.176690 TGTTTTTCTCTCCCCTTTGATCATTAC 59.823 37.037 0.00 0.00 0.00 1.89
2072 2579 5.373812 TTCTCTCCCCTTTGATCATTACC 57.626 43.478 0.00 0.00 0.00 2.85
2074 2581 4.410228 TCTCTCCCCTTTGATCATTACCTG 59.590 45.833 0.00 0.00 0.00 4.00
2075 2582 3.117888 TCTCCCCTTTGATCATTACCTGC 60.118 47.826 0.00 0.00 0.00 4.85
2076 2583 2.580322 TCCCCTTTGATCATTACCTGCA 59.420 45.455 0.00 0.00 0.00 4.41
2077 2584 3.011144 TCCCCTTTGATCATTACCTGCAA 59.989 43.478 0.00 0.00 0.00 4.08
2081 2588 2.804986 TGATCATTACCTGCAAGCCA 57.195 45.000 0.00 0.00 0.00 4.75
2082 2589 2.646930 TGATCATTACCTGCAAGCCAG 58.353 47.619 0.00 0.00 41.41 4.85
2089 2598 2.750637 CTGCAAGCCAGAGCCAGG 60.751 66.667 0.00 0.00 44.64 4.45
2100 2609 2.424956 CCAGAGCCAGGCATTTAGTTTC 59.575 50.000 15.80 0.00 0.00 2.78
2103 2612 1.812571 AGCCAGGCATTTAGTTTCGTG 59.187 47.619 15.80 0.00 0.00 4.35
2107 2616 3.236816 CAGGCATTTAGTTTCGTGCAAG 58.763 45.455 0.00 0.00 39.27 4.01
2116 2625 0.586319 TTTCGTGCAAGCGAGAAAGG 59.414 50.000 9.57 0.00 42.10 3.11
2117 2626 1.227999 TTCGTGCAAGCGAGAAAGGG 61.228 55.000 0.00 0.00 42.10 3.95
2131 2640 2.370849 AGAAAGGGAGTTCCGTGCTTAA 59.629 45.455 0.00 0.00 41.52 1.85
2132 2641 3.009143 AGAAAGGGAGTTCCGTGCTTAAT 59.991 43.478 0.00 0.00 41.52 1.40
2133 2642 3.434940 AAGGGAGTTCCGTGCTTAATT 57.565 42.857 0.00 0.00 41.52 1.40
2134 2643 4.563140 AAGGGAGTTCCGTGCTTAATTA 57.437 40.909 0.00 0.00 41.52 1.40
2135 2644 4.138487 AGGGAGTTCCGTGCTTAATTAG 57.862 45.455 0.00 0.00 41.52 1.73
2136 2645 3.118371 AGGGAGTTCCGTGCTTAATTAGG 60.118 47.826 0.00 0.00 41.52 2.69
2137 2646 3.203716 GGAGTTCCGTGCTTAATTAGGG 58.796 50.000 0.00 0.00 0.00 3.53
2138 2647 3.118519 GGAGTTCCGTGCTTAATTAGGGA 60.119 47.826 0.00 0.00 0.00 4.20
2139 2648 4.510571 GAGTTCCGTGCTTAATTAGGGAA 58.489 43.478 8.40 8.40 38.21 3.97
2225 2735 1.591183 CCCAAAAATCGGCCCAGTG 59.409 57.895 0.00 0.00 0.00 3.66
2226 2736 0.897863 CCCAAAAATCGGCCCAGTGA 60.898 55.000 0.00 0.00 0.00 3.41
2250 2761 1.170290 CCCAGAAGCCCGTTTTTCGT 61.170 55.000 0.00 0.00 37.94 3.85
2257 2768 0.585838 GCCCGTTTTTCGTCGGTTTA 59.414 50.000 0.00 0.00 44.51 2.01
2338 2871 2.176792 GCTTTGGCGCGAAAGAGG 59.823 61.111 38.41 20.33 35.30 3.69
2386 2924 1.305381 CCTCGTCTTCCCCCAGAGT 60.305 63.158 0.00 0.00 0.00 3.24
2394 2932 3.155167 CCCCCAGAGTACCTCGGC 61.155 72.222 0.00 0.00 35.36 5.54
2510 3128 1.672356 CACCAGTCCGAGCCCAAAG 60.672 63.158 0.00 0.00 0.00 2.77
2567 3209 1.790090 CGCCGAGCTCTGCTATCTCA 61.790 60.000 24.95 0.00 39.88 3.27
2614 3259 2.509336 CGATGGCCGAACGCTTCT 60.509 61.111 0.00 0.00 41.76 2.85
2672 3317 1.076632 CGCTCTAGGAGTGGGAGGT 60.077 63.158 0.68 0.00 36.63 3.85
2700 3345 1.002624 GTTCGAGGCCAACATCCCA 60.003 57.895 5.01 0.00 0.00 4.37
2749 3394 2.679716 GGGTGGAGGCTCAGCAAT 59.320 61.111 17.69 0.00 36.92 3.56
2752 3397 1.001641 GTGGAGGCTCAGCAATGGT 60.002 57.895 17.69 0.00 0.00 3.55
2755 3400 1.001641 GAGGCTCAGCAATGGTGGT 60.002 57.895 12.79 0.00 35.28 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.642432 CCAGGAGAAGAGAACATTATGTATGTA 58.358 37.037 0.00 0.00 46.75 2.29
3 4 6.933521 CCCAGGAGAAGAGAACATTATGTATG 59.066 42.308 0.00 0.00 40.26 2.39
4 5 6.846505 TCCCAGGAGAAGAGAACATTATGTAT 59.153 38.462 0.00 0.00 0.00 2.29
5 6 6.202331 TCCCAGGAGAAGAGAACATTATGTA 58.798 40.000 0.00 0.00 0.00 2.29
6 7 5.032846 TCCCAGGAGAAGAGAACATTATGT 58.967 41.667 0.00 0.00 0.00 2.29
7 8 5.620738 TCCCAGGAGAAGAGAACATTATG 57.379 43.478 0.00 0.00 0.00 1.90
8 9 5.966935 TCTTCCCAGGAGAAGAGAACATTAT 59.033 40.000 13.62 0.00 45.67 1.28
9 10 5.342017 TCTTCCCAGGAGAAGAGAACATTA 58.658 41.667 13.62 0.00 45.67 1.90
10 11 4.171234 TCTTCCCAGGAGAAGAGAACATT 58.829 43.478 13.62 0.00 45.67 2.71
11 12 3.796111 TCTTCCCAGGAGAAGAGAACAT 58.204 45.455 13.62 0.00 45.67 2.71
12 13 3.260269 TCTTCCCAGGAGAAGAGAACA 57.740 47.619 13.62 0.00 45.67 3.18
18 19 4.714308 ACTTAGTCATCTTCCCAGGAGAAG 59.286 45.833 10.15 10.15 43.88 2.85
19 20 4.467795 CACTTAGTCATCTTCCCAGGAGAA 59.532 45.833 0.00 0.00 0.00 2.87
20 21 4.026744 CACTTAGTCATCTTCCCAGGAGA 58.973 47.826 0.00 0.00 0.00 3.71
21 22 3.431486 GCACTTAGTCATCTTCCCAGGAG 60.431 52.174 0.00 0.00 0.00 3.69
22 23 2.501723 GCACTTAGTCATCTTCCCAGGA 59.498 50.000 0.00 0.00 0.00 3.86
23 24 2.237143 TGCACTTAGTCATCTTCCCAGG 59.763 50.000 0.00 0.00 0.00 4.45
24 25 3.196469 TCTGCACTTAGTCATCTTCCCAG 59.804 47.826 0.00 0.00 0.00 4.45
25 26 3.173151 TCTGCACTTAGTCATCTTCCCA 58.827 45.455 0.00 0.00 0.00 4.37
26 27 3.895232 TCTGCACTTAGTCATCTTCCC 57.105 47.619 0.00 0.00 0.00 3.97
27 28 9.547753 TTAATATTCTGCACTTAGTCATCTTCC 57.452 33.333 0.00 0.00 0.00 3.46
30 31 9.757227 GAGTTAATATTCTGCACTTAGTCATCT 57.243 33.333 0.00 0.00 0.00 2.90
31 32 9.757227 AGAGTTAATATTCTGCACTTAGTCATC 57.243 33.333 0.00 0.00 0.00 2.92
32 33 9.757227 GAGAGTTAATATTCTGCACTTAGTCAT 57.243 33.333 0.00 0.00 0.00 3.06
33 34 8.198109 GGAGAGTTAATATTCTGCACTTAGTCA 58.802 37.037 0.00 0.00 32.69 3.41
34 35 8.198109 TGGAGAGTTAATATTCTGCACTTAGTC 58.802 37.037 0.00 0.00 36.94 2.59
35 36 8.079211 TGGAGAGTTAATATTCTGCACTTAGT 57.921 34.615 0.00 0.00 36.94 2.24
36 37 9.553064 AATGGAGAGTTAATATTCTGCACTTAG 57.447 33.333 9.72 0.00 43.15 2.18
38 39 9.905713 TTAATGGAGAGTTAATATTCTGCACTT 57.094 29.630 9.72 8.58 43.15 3.16
39 40 9.331282 GTTAATGGAGAGTTAATATTCTGCACT 57.669 33.333 9.72 4.09 43.15 4.40
40 41 9.331282 AGTTAATGGAGAGTTAATATTCTGCAC 57.669 33.333 9.72 1.18 43.15 4.57
94 95 0.250727 AACCACAGTTGATCACCCCG 60.251 55.000 0.00 0.00 33.97 5.73
95 96 2.711542 CTAACCACAGTTGATCACCCC 58.288 52.381 0.00 0.00 36.68 4.95
115 116 9.493206 CATTATGCAAGTTTCATTATTTTTGGC 57.507 29.630 0.00 0.00 0.00 4.52
217 502 7.389053 GGTTGTCTGAGTCTTGATTAGTTGATT 59.611 37.037 0.00 0.00 0.00 2.57
231 516 0.537653 GCTAGGGGGTTGTCTGAGTC 59.462 60.000 0.00 0.00 0.00 3.36
278 563 7.581213 TTTCCTCTGTTTTTCTGCTTGATAA 57.419 32.000 0.00 0.00 0.00 1.75
303 588 2.232452 CGTATGCCCTTCTAGCTATGCT 59.768 50.000 0.00 0.00 43.41 3.79
304 589 2.611518 CGTATGCCCTTCTAGCTATGC 58.388 52.381 0.00 0.00 0.00 3.14
305 590 2.675317 GCCGTATGCCCTTCTAGCTATG 60.675 54.545 0.00 0.00 0.00 2.23
306 591 1.550976 GCCGTATGCCCTTCTAGCTAT 59.449 52.381 0.00 0.00 0.00 2.97
307 592 0.966920 GCCGTATGCCCTTCTAGCTA 59.033 55.000 0.00 0.00 0.00 3.32
308 593 0.760945 AGCCGTATGCCCTTCTAGCT 60.761 55.000 0.00 0.00 42.71 3.32
309 594 0.966920 TAGCCGTATGCCCTTCTAGC 59.033 55.000 0.00 0.00 42.71 3.42
310 595 3.963428 ATTAGCCGTATGCCCTTCTAG 57.037 47.619 0.00 0.00 42.71 2.43
311 596 4.219944 CACTATTAGCCGTATGCCCTTCTA 59.780 45.833 0.00 0.00 42.71 2.10
312 597 3.006967 CACTATTAGCCGTATGCCCTTCT 59.993 47.826 0.00 0.00 42.71 2.85
313 598 3.326747 CACTATTAGCCGTATGCCCTTC 58.673 50.000 0.00 0.00 42.71 3.46
314 599 2.038557 CCACTATTAGCCGTATGCCCTT 59.961 50.000 0.00 0.00 42.71 3.95
315 600 1.623811 CCACTATTAGCCGTATGCCCT 59.376 52.381 0.00 0.00 42.71 5.19
316 601 1.346722 ACCACTATTAGCCGTATGCCC 59.653 52.381 0.00 0.00 42.71 5.36
317 602 2.833631 ACCACTATTAGCCGTATGCC 57.166 50.000 0.00 0.00 42.71 4.40
321 606 9.565090 CACCTATATATACCACTATTAGCCGTA 57.435 37.037 0.00 0.00 0.00 4.02
322 607 7.014038 GCACCTATATATACCACTATTAGCCGT 59.986 40.741 0.00 0.00 0.00 5.68
323 608 7.230913 AGCACCTATATATACCACTATTAGCCG 59.769 40.741 0.00 0.00 0.00 5.52
324 609 8.480133 AGCACCTATATATACCACTATTAGCC 57.520 38.462 0.00 0.00 0.00 3.93
327 612 9.584008 GCCTAGCACCTATATATACCACTATTA 57.416 37.037 0.00 0.00 0.00 0.98
328 613 8.065627 TGCCTAGCACCTATATATACCACTATT 58.934 37.037 0.00 0.00 31.71 1.73
329 614 7.592736 TGCCTAGCACCTATATATACCACTAT 58.407 38.462 0.00 0.00 31.71 2.12
330 615 6.977104 TGCCTAGCACCTATATATACCACTA 58.023 40.000 0.00 0.00 31.71 2.74
331 616 5.838955 TGCCTAGCACCTATATATACCACT 58.161 41.667 0.00 0.00 31.71 4.00
332 617 5.657302 ACTGCCTAGCACCTATATATACCAC 59.343 44.000 0.00 0.00 33.79 4.16
333 618 5.838955 ACTGCCTAGCACCTATATATACCA 58.161 41.667 0.00 0.00 33.79 3.25
334 619 6.490721 CCTACTGCCTAGCACCTATATATACC 59.509 46.154 0.00 0.00 33.79 2.73
335 620 7.061688 ACCTACTGCCTAGCACCTATATATAC 58.938 42.308 0.00 0.00 33.79 1.47
336 621 7.222180 ACCTACTGCCTAGCACCTATATATA 57.778 40.000 0.00 0.00 33.79 0.86
337 622 6.093617 ACCTACTGCCTAGCACCTATATAT 57.906 41.667 0.00 0.00 33.79 0.86
338 623 5.531753 ACCTACTGCCTAGCACCTATATA 57.468 43.478 0.00 0.00 33.79 0.86
339 624 4.405756 ACCTACTGCCTAGCACCTATAT 57.594 45.455 0.00 0.00 33.79 0.86
340 625 3.897657 ACCTACTGCCTAGCACCTATA 57.102 47.619 0.00 0.00 33.79 1.31
341 626 2.777459 ACCTACTGCCTAGCACCTAT 57.223 50.000 0.00 0.00 33.79 2.57
342 627 2.024273 AGAACCTACTGCCTAGCACCTA 60.024 50.000 0.00 0.00 33.79 3.08
343 628 1.196012 GAACCTACTGCCTAGCACCT 58.804 55.000 0.00 0.00 33.79 4.00
344 629 1.196012 AGAACCTACTGCCTAGCACC 58.804 55.000 0.00 0.00 33.79 5.01
345 630 4.467198 TTAAGAACCTACTGCCTAGCAC 57.533 45.455 0.00 0.00 33.79 4.40
346 631 4.285003 TGTTTAAGAACCTACTGCCTAGCA 59.715 41.667 0.00 0.00 34.80 3.49
347 632 4.828829 TGTTTAAGAACCTACTGCCTAGC 58.171 43.478 0.00 0.00 34.80 3.42
348 633 6.071278 ACTCTGTTTAAGAACCTACTGCCTAG 60.071 42.308 0.00 0.00 33.37 3.02
349 634 5.778750 ACTCTGTTTAAGAACCTACTGCCTA 59.221 40.000 0.00 0.00 33.37 3.93
350 635 4.593634 ACTCTGTTTAAGAACCTACTGCCT 59.406 41.667 0.00 0.00 33.37 4.75
351 636 4.895961 ACTCTGTTTAAGAACCTACTGCC 58.104 43.478 0.00 0.00 33.37 4.85
352 637 6.689554 ACTACTCTGTTTAAGAACCTACTGC 58.310 40.000 0.00 0.00 33.37 4.40
353 638 9.790389 CATACTACTCTGTTTAAGAACCTACTG 57.210 37.037 0.00 0.00 33.37 2.74
354 639 8.468399 GCATACTACTCTGTTTAAGAACCTACT 58.532 37.037 0.00 0.00 33.37 2.57
355 640 7.431668 CGCATACTACTCTGTTTAAGAACCTAC 59.568 40.741 0.00 0.00 33.37 3.18
365 650 4.123497 TGATGCGCATACTACTCTGTTT 57.877 40.909 25.40 0.00 0.00 2.83
391 676 9.388506 CTTCACTTAATCCTATGTGTCAAATCT 57.611 33.333 0.00 0.00 35.61 2.40
393 678 9.520515 AACTTCACTTAATCCTATGTGTCAAAT 57.479 29.630 0.00 0.00 35.61 2.32
412 697 8.296713 ACCATGTAATGTTGTGATTAACTTCAC 58.703 33.333 2.78 2.78 44.81 3.18
417 702 6.747280 GCTCACCATGTAATGTTGTGATTAAC 59.253 38.462 0.00 0.00 44.81 2.01
418 703 6.658816 AGCTCACCATGTAATGTTGTGATTAA 59.341 34.615 0.00 0.00 44.81 1.40
421 706 4.592942 AGCTCACCATGTAATGTTGTGAT 58.407 39.130 0.00 0.00 44.81 3.06
434 737 2.092753 CCCATGTCAAGTAGCTCACCAT 60.093 50.000 0.00 0.00 0.00 3.55
476 779 7.648039 AAATAGGGTAACTGTTGTTCAACAA 57.352 32.000 17.14 0.00 37.59 2.83
486 789 7.562088 TGAACCAAAGAAAAATAGGGTAACTGT 59.438 33.333 0.00 0.00 0.00 3.55
529 832 2.620585 AGTGAGCAAAAGGTTGAGCTTC 59.379 45.455 0.00 0.00 37.48 3.86
600 903 5.509501 CGACAAACTTAGTACCACCCTTACA 60.510 44.000 0.00 0.00 0.00 2.41
609 912 4.563061 ACATGTCCGACAAACTTAGTACC 58.437 43.478 5.07 0.00 0.00 3.34
649 968 8.680903 GGATGAGTTTATGATGAGTTGTTCAAT 58.319 33.333 0.00 0.00 39.77 2.57
651 970 7.167535 TGGATGAGTTTATGATGAGTTGTTCA 58.832 34.615 0.00 0.00 40.85 3.18
652 971 7.615582 TGGATGAGTTTATGATGAGTTGTTC 57.384 36.000 0.00 0.00 0.00 3.18
653 972 7.448161 TGTTGGATGAGTTTATGATGAGTTGTT 59.552 33.333 0.00 0.00 0.00 2.83
654 973 6.942005 TGTTGGATGAGTTTATGATGAGTTGT 59.058 34.615 0.00 0.00 0.00 3.32
655 974 7.381766 TGTTGGATGAGTTTATGATGAGTTG 57.618 36.000 0.00 0.00 0.00 3.16
659 978 6.244654 TGGTTGTTGGATGAGTTTATGATGA 58.755 36.000 0.00 0.00 0.00 2.92
661 980 6.248433 ACTGGTTGTTGGATGAGTTTATGAT 58.752 36.000 0.00 0.00 0.00 2.45
716 1037 1.286849 AGGTAACAATAGCCCCAACCC 59.713 52.381 0.00 0.00 41.41 4.11
719 1040 2.568979 AGGAGGTAACAATAGCCCCAA 58.431 47.619 0.00 0.00 41.41 4.12
721 1042 3.288092 CAAAGGAGGTAACAATAGCCCC 58.712 50.000 0.00 0.00 41.41 5.80
824 1151 1.149401 GTCTCCCTAATGGCCTGCC 59.851 63.158 3.32 0.00 0.00 4.85
847 1176 9.252962 GCTTGGTTTGATGAATAATTAATCAGG 57.747 33.333 9.05 0.00 32.23 3.86
880 1212 2.039418 CTAGCAGTGGGGTACATGCTA 58.961 52.381 12.40 12.40 41.20 3.49
949 1281 1.807142 GTACTCTTGTTCCTTGCAGCC 59.193 52.381 0.00 0.00 0.00 4.85
1042 1374 1.450312 CATTGACGCACCTCCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
1071 1403 2.203337 TGGCACAAGTGTGGAGCC 60.203 61.111 13.10 8.67 45.72 4.70
1074 1406 1.227527 CTCGTGGCACAAGTGTGGA 60.228 57.895 19.09 3.71 44.16 4.02
1143 1475 2.202676 GTGAGGAGCTTCGAGGCG 60.203 66.667 14.34 0.00 37.29 5.52
1185 1517 3.315142 GATGGTGACCGCAGCCTCA 62.315 63.158 0.00 0.00 41.74 3.86
1328 1668 9.533253 CAGTTTACCAAATGAAAATTCAGAACT 57.467 29.630 1.98 0.00 41.08 3.01
1389 1749 7.625185 GCTTGCAGATTTACAACCTAAGAGAAG 60.625 40.741 0.00 0.00 0.00 2.85
1500 1860 4.644685 TCATAAGCCATAACCTTTGCCTTC 59.355 41.667 0.00 0.00 0.00 3.46
1506 1866 5.893824 CCCTTTCTCATAAGCCATAACCTTT 59.106 40.000 0.00 0.00 0.00 3.11
1522 1882 2.486370 GCATCCTAGCTTCCCCTTTCTC 60.486 54.545 0.00 0.00 0.00 2.87
1662 2034 7.549615 AAATTTAAACGAGGCTGTATAGTCC 57.450 36.000 0.00 0.00 0.00 3.85
1705 2077 0.322187 ACGGGAAACATGGTGCTACC 60.322 55.000 0.00 0.00 39.22 3.18
1737 2109 8.316946 TCATAATACCCATTCTCTTGCAGATAG 58.683 37.037 0.00 0.00 0.00 2.08
1828 2318 2.079925 CAAAAGAGGACTGCTGGTAGC 58.920 52.381 0.00 0.00 42.82 3.58
1892 2399 8.462016 CAGCATTTTAGTACAGGCTTAGAATTT 58.538 33.333 0.00 0.00 0.00 1.82
1894 2401 7.338710 TCAGCATTTTAGTACAGGCTTAGAAT 58.661 34.615 0.00 0.00 0.00 2.40
1895 2402 6.707290 TCAGCATTTTAGTACAGGCTTAGAA 58.293 36.000 0.00 0.00 0.00 2.10
1896 2403 6.294361 TCAGCATTTTAGTACAGGCTTAGA 57.706 37.500 0.00 0.00 0.00 2.10
1897 2404 6.985188 TTCAGCATTTTAGTACAGGCTTAG 57.015 37.500 0.00 0.00 0.00 2.18
1898 2405 7.109501 TGATTCAGCATTTTAGTACAGGCTTA 58.890 34.615 0.00 0.00 0.00 3.09
1899 2406 5.945784 TGATTCAGCATTTTAGTACAGGCTT 59.054 36.000 0.00 0.00 0.00 4.35
1925 2432 6.374417 AAACATATGTCTTCTACACCCTGT 57.626 37.500 9.23 0.00 42.09 4.00
1967 2474 2.858344 GCATTTCAGCATGCTTCATCAC 59.142 45.455 19.98 2.90 45.35 3.06
1968 2475 3.159353 GCATTTCAGCATGCTTCATCA 57.841 42.857 19.98 0.42 45.35 3.07
2005 2512 4.827304 TCTCTCATGATTCACTAGAGCG 57.173 45.455 16.83 8.41 34.89 5.03
2016 2523 7.399478 TCTTGGCATATCAGTATCTCTCATGAT 59.601 37.037 0.00 0.00 36.42 2.45
2018 2525 6.932947 TCTTGGCATATCAGTATCTCTCATG 58.067 40.000 0.00 0.00 0.00 3.07
2019 2526 7.736881 ATCTTGGCATATCAGTATCTCTCAT 57.263 36.000 0.00 0.00 0.00 2.90
2020 2527 8.693625 CATATCTTGGCATATCAGTATCTCTCA 58.306 37.037 0.00 0.00 0.00 3.27
2021 2528 8.694540 ACATATCTTGGCATATCAGTATCTCTC 58.305 37.037 0.00 0.00 0.00 3.20
2022 2529 8.606754 ACATATCTTGGCATATCAGTATCTCT 57.393 34.615 0.00 0.00 0.00 3.10
2023 2530 9.664332 AAACATATCTTGGCATATCAGTATCTC 57.336 33.333 0.00 0.00 0.00 2.75
2027 2534 9.851686 AGAAAAACATATCTTGGCATATCAGTA 57.148 29.630 0.00 0.00 0.00 2.74
2028 2535 8.757982 AGAAAAACATATCTTGGCATATCAGT 57.242 30.769 0.00 0.00 0.00 3.41
2029 2536 9.064706 AGAGAAAAACATATCTTGGCATATCAG 57.935 33.333 0.00 0.00 0.00 2.90
2030 2537 8.985315 AGAGAAAAACATATCTTGGCATATCA 57.015 30.769 0.00 0.00 0.00 2.15
2031 2538 8.510505 GGAGAGAAAAACATATCTTGGCATATC 58.489 37.037 0.00 0.00 0.00 1.63
2032 2539 7.449704 GGGAGAGAAAAACATATCTTGGCATAT 59.550 37.037 0.00 0.00 0.00 1.78
2033 2540 6.772716 GGGAGAGAAAAACATATCTTGGCATA 59.227 38.462 0.00 0.00 0.00 3.14
2034 2541 5.595952 GGGAGAGAAAAACATATCTTGGCAT 59.404 40.000 0.00 0.00 0.00 4.40
2035 2542 4.949856 GGGAGAGAAAAACATATCTTGGCA 59.050 41.667 0.00 0.00 0.00 4.92
2042 2549 7.413446 TGATCAAAGGGGAGAGAAAAACATAT 58.587 34.615 0.00 0.00 0.00 1.78
2046 2553 6.596309 AATGATCAAAGGGGAGAGAAAAAC 57.404 37.500 0.00 0.00 0.00 2.43
2058 2565 3.181483 GGCTTGCAGGTAATGATCAAAGG 60.181 47.826 0.00 0.00 0.00 3.11
2059 2566 3.444742 TGGCTTGCAGGTAATGATCAAAG 59.555 43.478 0.00 0.00 0.00 2.77
2071 2578 2.750637 CTGGCTCTGGCTTGCAGG 60.751 66.667 0.00 0.00 38.73 4.85
2072 2579 2.750637 CCTGGCTCTGGCTTGCAG 60.751 66.667 0.00 0.00 38.73 4.41
2075 2582 1.255667 AAATGCCTGGCTCTGGCTTG 61.256 55.000 21.03 0.00 46.43 4.01
2076 2583 0.332632 TAAATGCCTGGCTCTGGCTT 59.667 50.000 21.03 12.57 46.43 4.35
2077 2584 0.106819 CTAAATGCCTGGCTCTGGCT 60.107 55.000 21.03 1.14 46.43 4.75
2081 2588 2.290323 ACGAAACTAAATGCCTGGCTCT 60.290 45.455 21.03 4.24 0.00 4.09
2082 2589 2.084546 ACGAAACTAAATGCCTGGCTC 58.915 47.619 21.03 5.23 0.00 4.70
2089 2598 1.643810 CGCTTGCACGAAACTAAATGC 59.356 47.619 0.00 0.00 38.59 3.56
2095 2604 1.261619 CTTTCTCGCTTGCACGAAACT 59.738 47.619 0.87 0.00 42.39 2.66
2100 2609 1.630244 CTCCCTTTCTCGCTTGCACG 61.630 60.000 0.00 0.00 0.00 5.34
2103 2612 0.799393 GAACTCCCTTTCTCGCTTGC 59.201 55.000 0.00 0.00 0.00 4.01
2107 2616 1.014564 CACGGAACTCCCTTTCTCGC 61.015 60.000 0.00 0.00 0.00 5.03
2116 2625 3.118519 TCCCTAATTAAGCACGGAACTCC 60.119 47.826 0.00 0.00 0.00 3.85
2117 2626 4.133013 TCCCTAATTAAGCACGGAACTC 57.867 45.455 0.00 0.00 0.00 3.01
2131 2640 4.288626 TGCTCTTAGTTGTGGTTCCCTAAT 59.711 41.667 0.00 0.00 0.00 1.73
2132 2641 3.649023 TGCTCTTAGTTGTGGTTCCCTAA 59.351 43.478 0.00 0.00 0.00 2.69
2133 2642 3.244582 TGCTCTTAGTTGTGGTTCCCTA 58.755 45.455 0.00 0.00 0.00 3.53
2134 2643 2.054799 TGCTCTTAGTTGTGGTTCCCT 58.945 47.619 0.00 0.00 0.00 4.20
2135 2644 2.561478 TGCTCTTAGTTGTGGTTCCC 57.439 50.000 0.00 0.00 0.00 3.97
2136 2645 3.935828 GAGATGCTCTTAGTTGTGGTTCC 59.064 47.826 0.00 0.00 0.00 3.62
2137 2646 3.935828 GGAGATGCTCTTAGTTGTGGTTC 59.064 47.826 0.00 0.00 0.00 3.62
2138 2647 3.327757 TGGAGATGCTCTTAGTTGTGGTT 59.672 43.478 0.00 0.00 0.00 3.67
2139 2648 2.906389 TGGAGATGCTCTTAGTTGTGGT 59.094 45.455 0.00 0.00 0.00 4.16
2140 2649 3.529533 CTGGAGATGCTCTTAGTTGTGG 58.470 50.000 0.00 0.00 0.00 4.17
2141 2650 2.935201 GCTGGAGATGCTCTTAGTTGTG 59.065 50.000 0.00 0.00 0.00 3.33
2142 2651 2.093235 GGCTGGAGATGCTCTTAGTTGT 60.093 50.000 0.00 0.00 0.00 3.32
2143 2652 2.559440 GGCTGGAGATGCTCTTAGTTG 58.441 52.381 0.00 0.00 0.00 3.16
2144 2653 1.137872 CGGCTGGAGATGCTCTTAGTT 59.862 52.381 0.00 0.00 0.00 2.24
2166 2675 3.023735 GGGAGGGCCTGTTGGGAT 61.024 66.667 12.95 0.00 37.23 3.85
2225 2735 4.452733 CGGGCTTCTGGGGACGTC 62.453 72.222 7.13 7.13 0.00 4.34
2322 2855 2.176792 GCCTCTTTCGCGCCAAAG 59.823 61.111 19.85 19.85 35.06 2.77
2470 3072 1.170290 GCCAGCGGCGGGTTTTATAT 61.170 55.000 20.17 0.00 39.62 0.86
2498 3116 2.347490 GACTGCTTTGGGCTCGGA 59.653 61.111 0.00 0.00 42.39 4.55
2567 3209 4.735599 GGGAAGGGGAGGACGGGT 62.736 72.222 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.