Multiple sequence alignment - TraesCS2A01G209000

Loading Multiple Alignment...

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 TraesCS2A01G209000 chr2A 100.000 4307 0 0 1 4307 192071573 192067267 0.000000e+00 7954.0
1 TraesCS2A01G209000 chr2A 90.386 1321 101 10 884 2181 396394076 396395393 0.000000e+00 1712.0
2 TraesCS2A01G209000 chr2A 90.249 1323 103 10 884 2183 404688448 404687129 0.000000e+00 1705.0
3 TraesCS2A01G209000 chr2A 90.824 534 46 3 1 533 137529379 137528848 0.000000e+00 712.0
4 TraesCS2A01G209000 chr2A 93.194 382 24 2 877 1257 137528852 137528472 1.050000e-155 560.0
5 TraesCS2A01G209000 chr1A 96.918 3439 94 7 878 4307 267186910 267183475 0.000000e+00 5753.0
6 TraesCS2A01G209000 chr1A 96.173 1411 46 4 2178 3586 283717241 283715837 0.000000e+00 2300.0
7 TraesCS2A01G209000 chr1A 94.382 534 28 2 1 533 267187439 267186907 0.000000e+00 819.0
8 TraesCS2A01G209000 chr1A 94.813 347 17 1 533 878 147500405 147500059 1.360000e-149 540.0
9 TraesCS2A01G209000 chr5A 97.192 1674 44 3 1914 3586 131732883 131734554 0.000000e+00 2828.0
10 TraesCS2A01G209000 chr5A 95.652 1334 38 2 2178 3511 65463957 65465270 0.000000e+00 2124.0
11 TraesCS2A01G209000 chr5A 95.072 345 16 1 534 877 642855896 642855552 3.790000e-150 542.0
12 TraesCS2A01G209000 chr5A 94.813 347 17 1 533 878 26619083 26618737 1.360000e-149 540.0
13 TraesCS2A01G209000 chr7A 96.478 1675 54 4 1914 3586 360564760 360563089 0.000000e+00 2761.0
14 TraesCS2A01G209000 chr7A 97.031 943 26 2 1914 2855 331644874 331645815 0.000000e+00 1585.0
15 TraesCS2A01G209000 chr3A 95.576 1650 72 1 877 2525 438528865 438530514 0.000000e+00 2641.0
16 TraesCS2A01G209000 chr3A 96.380 1409 41 6 2906 4307 438536530 438537935 0.000000e+00 2311.0
17 TraesCS2A01G209000 chr3A 92.932 382 25 2 153 533 438528489 438528869 4.870000e-154 555.0
18 TraesCS2A01G209000 chr3A 93.252 163 8 3 1 162 438520959 438521119 2.000000e-58 237.0
19 TraesCS2A01G209000 chr5B 96.776 1427 45 1 905 2331 489108303 489106878 0.000000e+00 2379.0
20 TraesCS2A01G209000 chr5B 88.722 1330 96 20 879 2183 570949151 570950451 0.000000e+00 1576.0
21 TraesCS2A01G209000 chr5B 95.014 722 29 3 3589 4304 266958457 266959177 0.000000e+00 1127.0
22 TraesCS2A01G209000 chr5B 93.346 541 25 4 1 534 489108840 489108304 0.000000e+00 789.0
23 TraesCS2A01G209000 chr5B 94.813 347 17 1 533 878 407637020 407636674 1.360000e-149 540.0
24 TraesCS2A01G209000 chr5B 86.538 312 39 3 220 530 205704992 205705301 1.480000e-89 340.0
25 TraesCS2A01G209000 chr6A 96.309 1409 51 1 2178 3586 360132278 360130871 0.000000e+00 2313.0
26 TraesCS2A01G209000 chr6A 89.513 534 53 3 1 533 173595817 173596348 0.000000e+00 673.0
27 TraesCS2A01G209000 chr4B 96.186 1416 45 4 2178 3586 253902342 253903755 0.000000e+00 2307.0
28 TraesCS2A01G209000 chr4B 89.533 1328 108 12 884 2183 414686844 414688168 0.000000e+00 1653.0
29 TraesCS2A01G209000 chr4B 95.261 211 10 0 3643 3853 152082419 152082209 6.900000e-88 335.0
30 TraesCS2A01G209000 chr3B 95.957 1410 52 5 2178 3586 655513511 655514916 0.000000e+00 2283.0
31 TraesCS2A01G209000 chr3B 90.415 1085 86 9 1115 2183 387731809 387730727 0.000000e+00 1411.0
32 TraesCS2A01G209000 chr3B 94.839 620 23 5 3695 4307 473400878 473401495 0.000000e+00 959.0
33 TraesCS2A01G209000 chr3B 86.667 315 38 4 220 533 387732441 387732130 3.190000e-91 346.0
34 TraesCS2A01G209000 chr2B 90.537 1321 100 11 884 2183 626799319 626800635 0.000000e+00 1724.0
35 TraesCS2A01G209000 chr1B 90.296 1319 106 16 884 2183 399299597 399298282 0.000000e+00 1707.0
36 TraesCS2A01G209000 chr1B 95.349 43 2 0 144 186 399300693 399300651 7.730000e-08 69.4
37 TraesCS2A01G209000 chr4D 92.241 1160 74 4 1040 2183 196639371 196640530 0.000000e+00 1629.0
38 TraesCS2A01G209000 chr4D 94.813 347 16 2 533 878 67180463 67180808 1.360000e-149 540.0
39 TraesCS2A01G209000 chr6D 96.953 722 15 3 3589 4304 73831972 73832692 0.000000e+00 1205.0
40 TraesCS2A01G209000 chr6D 95.448 725 21 4 3589 4307 256247456 256248174 0.000000e+00 1146.0
41 TraesCS2A01G209000 chr6B 95.862 725 22 4 3589 4307 199015518 199014796 0.000000e+00 1166.0
42 TraesCS2A01G209000 chr7B 95.586 725 24 4 3589 4307 355694697 355693975 0.000000e+00 1155.0
43 TraesCS2A01G209000 chr3D 94.195 534 29 2 1 533 297922099 297921567 0.000000e+00 813.0
44 TraesCS2A01G209000 chr3D 92.800 375 18 3 875 1241 297921574 297921201 6.340000e-148 534.0
45 TraesCS2A01G209000 chr2D 95.101 347 16 1 533 878 119417449 119417795 2.930000e-151 545.0
46 TraesCS2A01G209000 chr2D 94.798 346 17 1 533 877 472431459 472431114 4.900000e-149 538.0
47 TraesCS2A01G209000 chr7D 93.855 358 19 3 524 878 245465332 245464975 1.760000e-148 536.0
48 TraesCS2A01G209000 chr7D 94.318 352 17 3 533 882 476900907 476900557 1.760000e-148 536.0
49 TraesCS2A01G209000 chr4A 91.892 333 25 2 1 332 722504887 722504556 8.440000e-127 464.0
50 TraesCS2A01G209000 chr4A 89.524 210 17 3 325 533 722501516 722501311 1.190000e-65 261.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G209000 chr2A 192067267 192071573 4306 True 7954.0 7954 100.0000 1 4307 1 chr2A.!!$R1 4306
1 TraesCS2A01G209000 chr2A 396394076 396395393 1317 False 1712.0 1712 90.3860 884 2181 1 chr2A.!!$F1 1297
2 TraesCS2A01G209000 chr2A 404687129 404688448 1319 True 1705.0 1705 90.2490 884 2183 1 chr2A.!!$R2 1299
3 TraesCS2A01G209000 chr2A 137528472 137529379 907 True 636.0 712 92.0090 1 1257 2 chr2A.!!$R3 1256
4 TraesCS2A01G209000 chr1A 267183475 267187439 3964 True 3286.0 5753 95.6500 1 4307 2 chr1A.!!$R3 4306
5 TraesCS2A01G209000 chr1A 283715837 283717241 1404 True 2300.0 2300 96.1730 2178 3586 1 chr1A.!!$R2 1408
6 TraesCS2A01G209000 chr5A 131732883 131734554 1671 False 2828.0 2828 97.1920 1914 3586 1 chr5A.!!$F2 1672
7 TraesCS2A01G209000 chr5A 65463957 65465270 1313 False 2124.0 2124 95.6520 2178 3511 1 chr5A.!!$F1 1333
8 TraesCS2A01G209000 chr7A 360563089 360564760 1671 True 2761.0 2761 96.4780 1914 3586 1 chr7A.!!$R1 1672
9 TraesCS2A01G209000 chr7A 331644874 331645815 941 False 1585.0 1585 97.0310 1914 2855 1 chr7A.!!$F1 941
10 TraesCS2A01G209000 chr3A 438536530 438537935 1405 False 2311.0 2311 96.3800 2906 4307 1 chr3A.!!$F2 1401
11 TraesCS2A01G209000 chr3A 438528489 438530514 2025 False 1598.0 2641 94.2540 153 2525 2 chr3A.!!$F3 2372
12 TraesCS2A01G209000 chr5B 489106878 489108840 1962 True 1584.0 2379 95.0610 1 2331 2 chr5B.!!$R2 2330
13 TraesCS2A01G209000 chr5B 570949151 570950451 1300 False 1576.0 1576 88.7220 879 2183 1 chr5B.!!$F3 1304
14 TraesCS2A01G209000 chr5B 266958457 266959177 720 False 1127.0 1127 95.0140 3589 4304 1 chr5B.!!$F2 715
15 TraesCS2A01G209000 chr6A 360130871 360132278 1407 True 2313.0 2313 96.3090 2178 3586 1 chr6A.!!$R1 1408
16 TraesCS2A01G209000 chr6A 173595817 173596348 531 False 673.0 673 89.5130 1 533 1 chr6A.!!$F1 532
17 TraesCS2A01G209000 chr4B 253902342 253903755 1413 False 2307.0 2307 96.1860 2178 3586 1 chr4B.!!$F1 1408
18 TraesCS2A01G209000 chr4B 414686844 414688168 1324 False 1653.0 1653 89.5330 884 2183 1 chr4B.!!$F2 1299
19 TraesCS2A01G209000 chr3B 655513511 655514916 1405 False 2283.0 2283 95.9570 2178 3586 1 chr3B.!!$F2 1408
20 TraesCS2A01G209000 chr3B 473400878 473401495 617 False 959.0 959 94.8390 3695 4307 1 chr3B.!!$F1 612
21 TraesCS2A01G209000 chr3B 387730727 387732441 1714 True 878.5 1411 88.5410 220 2183 2 chr3B.!!$R1 1963
22 TraesCS2A01G209000 chr2B 626799319 626800635 1316 False 1724.0 1724 90.5370 884 2183 1 chr2B.!!$F1 1299
23 TraesCS2A01G209000 chr1B 399298282 399300693 2411 True 888.2 1707 92.8225 144 2183 2 chr1B.!!$R1 2039
24 TraesCS2A01G209000 chr4D 196639371 196640530 1159 False 1629.0 1629 92.2410 1040 2183 1 chr4D.!!$F2 1143
25 TraesCS2A01G209000 chr6D 73831972 73832692 720 False 1205.0 1205 96.9530 3589 4304 1 chr6D.!!$F1 715
26 TraesCS2A01G209000 chr6D 256247456 256248174 718 False 1146.0 1146 95.4480 3589 4307 1 chr6D.!!$F2 718
27 TraesCS2A01G209000 chr6B 199014796 199015518 722 True 1166.0 1166 95.8620 3589 4307 1 chr6B.!!$R1 718
28 TraesCS2A01G209000 chr7B 355693975 355694697 722 True 1155.0 1155 95.5860 3589 4307 1 chr7B.!!$R1 718
29 TraesCS2A01G209000 chr3D 297921201 297922099 898 True 673.5 813 93.4975 1 1241 2 chr3D.!!$R1 1240
30 TraesCS2A01G209000 chr4A 722501311 722504887 3576 True 362.5 464 90.7080 1 533 2 chr4A.!!$R1 532

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
549 4317 0.038166 GTGAGGGTGCTTGGATCCAA 59.962 55.000 25.53 25.53 0.00 3.53 F
614 4382 0.779997 AATTCCAAGCACCCCTGACT 59.220 50.000 0.00 0.00 0.00 3.41 F
822 4590 0.841961 AAGCATGGATGAGGCTAGCA 59.158 50.000 18.24 0.00 42.15 3.49 F
1681 5663 1.066303 TCGCATGTTTGCCTTCGTTTT 59.934 42.857 0.00 0.00 46.57 2.43 F
2865 6862 1.228154 GGCGGGAGTCTGGTTTGTT 60.228 57.895 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 5479 0.721718 GCACGGCGAGGCAATATATC 59.278 55.000 16.62 0.00 0.00 1.63 R
2385 6378 1.750399 GCGCACCTGATTCCACCAT 60.750 57.895 0.30 0.00 0.00 3.55 R
2745 6742 8.514594 TCATTTCTAAAATAGAAGTGCACCAAG 58.485 33.333 14.63 0.00 46.17 3.61 R
3301 7299 4.441634 GGAGCAACCTTAGCGATTCTAGAA 60.442 45.833 7.82 7.82 37.01 2.10 R
4217 8229 4.766891 CCATGGTAGAACATTCAACAAGGT 59.233 41.667 2.57 0.00 0.00 3.50 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
88 89 0.539986 GGACGGTAGATCTTGGCCAA 59.460 55.000 19.25 19.25 0.00 4.52
420 4188 2.025767 CTGCCTCCTGCGTCAGCTAT 62.026 60.000 0.00 0.00 45.60 2.97
443 4211 2.358247 GGTGGGTCGACGCATGTT 60.358 61.111 33.87 0.00 40.93 2.71
528 4296 1.140407 CGCTCGTTGGCTGCTACTAC 61.140 60.000 0.00 0.00 0.00 2.73
529 4297 0.173708 GCTCGTTGGCTGCTACTACT 59.826 55.000 0.00 0.00 0.00 2.57
530 4298 1.914634 CTCGTTGGCTGCTACTACTG 58.085 55.000 0.00 0.00 0.00 2.74
531 4299 1.202582 CTCGTTGGCTGCTACTACTGT 59.797 52.381 0.00 0.00 0.00 3.55
532 4300 1.067846 TCGTTGGCTGCTACTACTGTG 60.068 52.381 0.00 0.00 0.00 3.66
533 4301 1.067846 CGTTGGCTGCTACTACTGTGA 60.068 52.381 0.00 0.00 0.00 3.58
534 4302 2.611518 GTTGGCTGCTACTACTGTGAG 58.388 52.381 0.00 0.00 0.00 3.51
535 4303 1.186200 TGGCTGCTACTACTGTGAGG 58.814 55.000 0.00 0.00 0.00 3.86
536 4304 0.461961 GGCTGCTACTACTGTGAGGG 59.538 60.000 0.00 0.00 0.00 4.30
537 4305 1.187087 GCTGCTACTACTGTGAGGGT 58.813 55.000 0.00 0.00 0.00 4.34
538 4306 1.134965 GCTGCTACTACTGTGAGGGTG 60.135 57.143 0.00 0.00 0.00 4.61
539 4307 0.895530 TGCTACTACTGTGAGGGTGC 59.104 55.000 0.00 0.00 0.00 5.01
540 4308 1.187087 GCTACTACTGTGAGGGTGCT 58.813 55.000 0.00 0.00 0.00 4.40
541 4309 1.550976 GCTACTACTGTGAGGGTGCTT 59.449 52.381 0.00 0.00 0.00 3.91
542 4310 2.675317 GCTACTACTGTGAGGGTGCTTG 60.675 54.545 0.00 0.00 0.00 4.01
543 4311 0.687354 ACTACTGTGAGGGTGCTTGG 59.313 55.000 0.00 0.00 0.00 3.61
544 4312 0.976641 CTACTGTGAGGGTGCTTGGA 59.023 55.000 0.00 0.00 0.00 3.53
545 4313 1.556911 CTACTGTGAGGGTGCTTGGAT 59.443 52.381 0.00 0.00 0.00 3.41
546 4314 0.326264 ACTGTGAGGGTGCTTGGATC 59.674 55.000 0.00 0.00 0.00 3.36
547 4315 0.393537 CTGTGAGGGTGCTTGGATCC 60.394 60.000 4.20 4.20 0.00 3.36
548 4316 1.133181 TGTGAGGGTGCTTGGATCCA 61.133 55.000 11.44 11.44 0.00 3.41
549 4317 0.038166 GTGAGGGTGCTTGGATCCAA 59.962 55.000 25.53 25.53 0.00 3.53
564 4332 8.567285 CTTGGATCCAAGTGACTTATTTTAGT 57.433 34.615 36.68 0.00 45.91 2.24
565 4333 8.561738 TTGGATCCAAGTGACTTATTTTAGTC 57.438 34.615 23.63 0.00 43.86 2.59
566 4334 7.918076 TGGATCCAAGTGACTTATTTTAGTCT 58.082 34.615 13.46 0.00 43.92 3.24
567 4335 7.824289 TGGATCCAAGTGACTTATTTTAGTCTG 59.176 37.037 13.46 0.00 43.92 3.51
568 4336 8.041323 GGATCCAAGTGACTTATTTTAGTCTGA 58.959 37.037 6.95 0.00 43.92 3.27
569 4337 8.779354 ATCCAAGTGACTTATTTTAGTCTGAC 57.221 34.615 0.00 0.00 43.92 3.51
570 4338 7.963532 TCCAAGTGACTTATTTTAGTCTGACT 58.036 34.615 15.57 15.57 43.92 3.41
571 4339 9.085645 TCCAAGTGACTTATTTTAGTCTGACTA 57.914 33.333 13.34 13.34 43.92 2.59
572 4340 9.706691 CCAAGTGACTTATTTTAGTCTGACTAA 57.293 33.333 22.80 22.80 43.92 2.24
591 4359 9.308318 CTGACTAAAAATAGTCTCTTAAGAGGC 57.692 37.037 26.38 26.38 46.62 4.70
602 4370 7.923414 GTCTCTTAAGAGGCTAAAATTCCAA 57.077 36.000 26.40 3.98 43.13 3.53
603 4371 7.980062 GTCTCTTAAGAGGCTAAAATTCCAAG 58.020 38.462 26.40 0.89 43.13 3.61
604 4372 6.599638 TCTCTTAAGAGGCTAAAATTCCAAGC 59.400 38.462 28.09 0.00 42.30 4.01
605 4373 6.245408 TCTTAAGAGGCTAAAATTCCAAGCA 58.755 36.000 0.00 0.00 38.01 3.91
606 4374 4.790765 AAGAGGCTAAAATTCCAAGCAC 57.209 40.909 8.39 3.37 38.01 4.40
607 4375 3.092301 AGAGGCTAAAATTCCAAGCACC 58.908 45.455 8.39 0.00 38.01 5.01
608 4376 2.166459 GAGGCTAAAATTCCAAGCACCC 59.834 50.000 8.39 0.00 38.01 4.61
609 4377 1.207089 GGCTAAAATTCCAAGCACCCC 59.793 52.381 8.39 0.00 38.01 4.95
610 4378 2.179427 GCTAAAATTCCAAGCACCCCT 58.821 47.619 2.67 0.00 36.26 4.79
611 4379 2.094026 GCTAAAATTCCAAGCACCCCTG 60.094 50.000 2.67 0.00 36.26 4.45
612 4380 2.397044 AAAATTCCAAGCACCCCTGA 57.603 45.000 0.00 0.00 0.00 3.86
613 4381 1.632589 AAATTCCAAGCACCCCTGAC 58.367 50.000 0.00 0.00 0.00 3.51
614 4382 0.779997 AATTCCAAGCACCCCTGACT 59.220 50.000 0.00 0.00 0.00 3.41
615 4383 1.668826 ATTCCAAGCACCCCTGACTA 58.331 50.000 0.00 0.00 0.00 2.59
616 4384 1.440618 TTCCAAGCACCCCTGACTAA 58.559 50.000 0.00 0.00 0.00 2.24
617 4385 1.440618 TCCAAGCACCCCTGACTAAA 58.559 50.000 0.00 0.00 0.00 1.85
618 4386 1.351017 TCCAAGCACCCCTGACTAAAG 59.649 52.381 0.00 0.00 0.00 1.85
619 4387 1.351017 CCAAGCACCCCTGACTAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
620 4388 2.616510 CCAAGCACCCCTGACTAAAGAG 60.617 54.545 0.00 0.00 0.00 2.85
621 4389 1.280457 AGCACCCCTGACTAAAGAGG 58.720 55.000 0.00 0.00 0.00 3.69
625 4393 3.013682 CCCTGACTAAAGAGGGGCT 57.986 57.895 0.00 0.00 44.88 5.19
626 4394 2.176247 CCCTGACTAAAGAGGGGCTA 57.824 55.000 0.00 0.00 44.88 3.93
627 4395 2.478292 CCCTGACTAAAGAGGGGCTAA 58.522 52.381 0.00 0.00 44.88 3.09
628 4396 2.844348 CCCTGACTAAAGAGGGGCTAAA 59.156 50.000 0.00 0.00 44.88 1.85
629 4397 3.265995 CCCTGACTAAAGAGGGGCTAAAA 59.734 47.826 0.00 0.00 44.88 1.52
630 4398 4.262617 CCTGACTAAAGAGGGGCTAAAAC 58.737 47.826 0.00 0.00 0.00 2.43
631 4399 4.019231 CCTGACTAAAGAGGGGCTAAAACT 60.019 45.833 0.00 0.00 0.00 2.66
632 4400 5.189145 CCTGACTAAAGAGGGGCTAAAACTA 59.811 44.000 0.00 0.00 0.00 2.24
633 4401 6.295719 TGACTAAAGAGGGGCTAAAACTAG 57.704 41.667 0.00 0.00 0.00 2.57
634 4402 5.783875 TGACTAAAGAGGGGCTAAAACTAGT 59.216 40.000 0.00 0.00 0.00 2.57
635 4403 6.070938 TGACTAAAGAGGGGCTAAAACTAGTC 60.071 42.308 0.00 0.00 0.00 2.59
636 4404 6.024247 ACTAAAGAGGGGCTAAAACTAGTCT 58.976 40.000 0.00 0.00 0.00 3.24
637 4405 5.423704 AAAGAGGGGCTAAAACTAGTCTC 57.576 43.478 0.00 0.00 0.00 3.36
638 4406 3.025262 AGAGGGGCTAAAACTAGTCTCG 58.975 50.000 0.00 0.00 0.00 4.04
639 4407 3.022406 GAGGGGCTAAAACTAGTCTCGA 58.978 50.000 0.00 0.00 0.00 4.04
640 4408 3.025262 AGGGGCTAAAACTAGTCTCGAG 58.975 50.000 5.93 5.93 0.00 4.04
641 4409 3.022406 GGGGCTAAAACTAGTCTCGAGA 58.978 50.000 12.08 12.08 0.00 4.04
642 4410 3.181488 GGGGCTAAAACTAGTCTCGAGAC 60.181 52.174 33.52 33.52 45.08 3.36
666 4434 5.366829 AAAATGTTTTAGTCAGCGGTACC 57.633 39.130 0.16 0.16 0.00 3.34
667 4435 2.460757 TGTTTTAGTCAGCGGTACCC 57.539 50.000 6.25 0.00 0.00 3.69
668 4436 1.002315 TGTTTTAGTCAGCGGTACCCC 59.998 52.381 6.25 0.00 0.00 4.95
669 4437 1.277273 GTTTTAGTCAGCGGTACCCCT 59.723 52.381 6.25 0.00 0.00 4.79
670 4438 2.497273 GTTTTAGTCAGCGGTACCCCTA 59.503 50.000 6.25 0.00 0.00 3.53
671 4439 2.761786 TTAGTCAGCGGTACCCCTAT 57.238 50.000 6.25 0.00 0.00 2.57
672 4440 2.761786 TAGTCAGCGGTACCCCTATT 57.238 50.000 6.25 0.00 0.00 1.73
673 4441 2.761786 AGTCAGCGGTACCCCTATTA 57.238 50.000 6.25 0.00 0.00 0.98
674 4442 3.036452 AGTCAGCGGTACCCCTATTAA 57.964 47.619 6.25 0.00 0.00 1.40
675 4443 3.377573 AGTCAGCGGTACCCCTATTAAA 58.622 45.455 6.25 0.00 0.00 1.52
676 4444 3.776417 AGTCAGCGGTACCCCTATTAAAA 59.224 43.478 6.25 0.00 0.00 1.52
677 4445 4.411212 AGTCAGCGGTACCCCTATTAAAAT 59.589 41.667 6.25 0.00 0.00 1.82
678 4446 4.514066 GTCAGCGGTACCCCTATTAAAATG 59.486 45.833 6.25 0.00 0.00 2.32
679 4447 4.164604 TCAGCGGTACCCCTATTAAAATGT 59.835 41.667 6.25 0.00 0.00 2.71
680 4448 4.274950 CAGCGGTACCCCTATTAAAATGTG 59.725 45.833 6.25 0.00 0.00 3.21
681 4449 3.566742 GCGGTACCCCTATTAAAATGTGG 59.433 47.826 6.25 0.00 0.00 4.17
682 4450 4.686670 GCGGTACCCCTATTAAAATGTGGA 60.687 45.833 6.25 0.00 0.00 4.02
683 4451 5.627135 CGGTACCCCTATTAAAATGTGGAT 58.373 41.667 6.25 0.00 0.00 3.41
684 4452 6.066032 CGGTACCCCTATTAAAATGTGGATT 58.934 40.000 6.25 0.00 0.00 3.01
685 4453 7.225725 CGGTACCCCTATTAAAATGTGGATTA 58.774 38.462 6.25 0.00 0.00 1.75
686 4454 7.389607 CGGTACCCCTATTAAAATGTGGATTAG 59.610 40.741 6.25 0.00 0.00 1.73
687 4455 8.222637 GGTACCCCTATTAAAATGTGGATTAGT 58.777 37.037 0.00 0.00 0.00 2.24
688 4456 9.281371 GTACCCCTATTAAAATGTGGATTAGTC 57.719 37.037 0.00 0.00 0.00 2.59
689 4457 7.295340 ACCCCTATTAAAATGTGGATTAGTCC 58.705 38.462 0.00 0.00 45.31 3.85
690 4458 7.130442 ACCCCTATTAAAATGTGGATTAGTCCT 59.870 37.037 5.79 0.00 45.32 3.85
691 4459 7.665974 CCCCTATTAAAATGTGGATTAGTCCTC 59.334 40.741 5.79 2.58 45.32 3.71
692 4460 8.440771 CCCTATTAAAATGTGGATTAGTCCTCT 58.559 37.037 5.79 0.00 45.32 3.69
693 4461 9.495572 CCTATTAAAATGTGGATTAGTCCTCTC 57.504 37.037 5.79 0.00 45.32 3.20
696 4464 6.882768 AAAATGTGGATTAGTCCTCTCTCT 57.117 37.500 5.79 0.00 45.32 3.10
697 4465 6.478512 AAATGTGGATTAGTCCTCTCTCTC 57.521 41.667 5.79 0.00 45.32 3.20
698 4466 3.904717 TGTGGATTAGTCCTCTCTCTCC 58.095 50.000 5.79 0.00 45.32 3.71
699 4467 3.529734 TGTGGATTAGTCCTCTCTCTCCT 59.470 47.826 5.79 0.00 45.32 3.69
700 4468 4.142038 GTGGATTAGTCCTCTCTCTCCTC 58.858 52.174 5.79 0.00 45.32 3.71
701 4469 3.788708 TGGATTAGTCCTCTCTCTCCTCA 59.211 47.826 5.79 0.00 45.32 3.86
702 4470 4.418526 TGGATTAGTCCTCTCTCTCCTCAT 59.581 45.833 5.79 0.00 45.32 2.90
703 4471 5.103301 TGGATTAGTCCTCTCTCTCCTCATT 60.103 44.000 5.79 0.00 45.32 2.57
704 4472 5.838521 GGATTAGTCCTCTCTCTCCTCATTT 59.161 44.000 0.00 0.00 41.60 2.32
705 4473 7.007723 GGATTAGTCCTCTCTCTCCTCATTTA 58.992 42.308 0.00 0.00 41.60 1.40
706 4474 7.507616 GGATTAGTCCTCTCTCTCCTCATTTAA 59.492 40.741 0.00 0.00 41.60 1.52
707 4475 9.088987 GATTAGTCCTCTCTCTCCTCATTTAAT 57.911 37.037 0.00 0.00 0.00 1.40
708 4476 8.846423 TTAGTCCTCTCTCTCCTCATTTAATT 57.154 34.615 0.00 0.00 0.00 1.40
709 4477 7.360113 AGTCCTCTCTCTCCTCATTTAATTC 57.640 40.000 0.00 0.00 0.00 2.17
710 4478 6.326323 AGTCCTCTCTCTCCTCATTTAATTCC 59.674 42.308 0.00 0.00 0.00 3.01
711 4479 6.326323 GTCCTCTCTCTCCTCATTTAATTCCT 59.674 42.308 0.00 0.00 0.00 3.36
712 4480 6.553100 TCCTCTCTCTCCTCATTTAATTCCTC 59.447 42.308 0.00 0.00 0.00 3.71
713 4481 6.554605 CCTCTCTCTCCTCATTTAATTCCTCT 59.445 42.308 0.00 0.00 0.00 3.69
714 4482 7.071071 CCTCTCTCTCCTCATTTAATTCCTCTT 59.929 40.741 0.00 0.00 0.00 2.85
715 4483 8.017418 TCTCTCTCCTCATTTAATTCCTCTTC 57.983 38.462 0.00 0.00 0.00 2.87
716 4484 7.843760 TCTCTCTCCTCATTTAATTCCTCTTCT 59.156 37.037 0.00 0.00 0.00 2.85
717 4485 8.386012 TCTCTCCTCATTTAATTCCTCTTCTT 57.614 34.615 0.00 0.00 0.00 2.52
718 4486 8.830741 TCTCTCCTCATTTAATTCCTCTTCTTT 58.169 33.333 0.00 0.00 0.00 2.52
727 4495 9.860898 ATTTAATTCCTCTTCTTTAACACATGC 57.139 29.630 0.00 0.00 0.00 4.06
728 4496 5.551760 ATTCCTCTTCTTTAACACATGCG 57.448 39.130 0.00 0.00 0.00 4.73
729 4497 4.265904 TCCTCTTCTTTAACACATGCGA 57.734 40.909 0.00 0.00 0.00 5.10
730 4498 4.245660 TCCTCTTCTTTAACACATGCGAG 58.754 43.478 0.00 0.00 0.00 5.03
731 4499 3.997021 CCTCTTCTTTAACACATGCGAGT 59.003 43.478 0.00 0.00 0.00 4.18
732 4500 4.452455 CCTCTTCTTTAACACATGCGAGTT 59.548 41.667 0.00 0.00 0.00 3.01
733 4501 5.049405 CCTCTTCTTTAACACATGCGAGTTT 60.049 40.000 4.42 0.00 0.00 2.66
734 4502 6.371809 TCTTCTTTAACACATGCGAGTTTT 57.628 33.333 4.42 0.00 0.00 2.43
735 4503 6.198687 TCTTCTTTAACACATGCGAGTTTTG 58.801 36.000 4.42 0.00 0.00 2.44
736 4504 4.854399 TCTTTAACACATGCGAGTTTTGG 58.146 39.130 4.42 0.00 0.00 3.28
737 4505 4.576873 TCTTTAACACATGCGAGTTTTGGA 59.423 37.500 4.42 0.00 0.00 3.53
738 4506 5.240623 TCTTTAACACATGCGAGTTTTGGAT 59.759 36.000 4.42 0.00 0.00 3.41
739 4507 5.446143 TTAACACATGCGAGTTTTGGATT 57.554 34.783 4.42 0.00 0.00 3.01
740 4508 6.561737 TTAACACATGCGAGTTTTGGATTA 57.438 33.333 4.42 0.00 0.00 1.75
741 4509 4.685169 ACACATGCGAGTTTTGGATTAG 57.315 40.909 0.00 0.00 0.00 1.73
742 4510 4.323417 ACACATGCGAGTTTTGGATTAGA 58.677 39.130 0.00 0.00 0.00 2.10
743 4511 4.393062 ACACATGCGAGTTTTGGATTAGAG 59.607 41.667 0.00 0.00 0.00 2.43
744 4512 3.941483 ACATGCGAGTTTTGGATTAGAGG 59.059 43.478 0.00 0.00 0.00 3.69
745 4513 2.985896 TGCGAGTTTTGGATTAGAGGG 58.014 47.619 0.00 0.00 0.00 4.30
746 4514 2.304761 TGCGAGTTTTGGATTAGAGGGT 59.695 45.455 0.00 0.00 0.00 4.34
747 4515 3.244770 TGCGAGTTTTGGATTAGAGGGTT 60.245 43.478 0.00 0.00 0.00 4.11
748 4516 3.756963 GCGAGTTTTGGATTAGAGGGTTT 59.243 43.478 0.00 0.00 0.00 3.27
749 4517 4.379499 GCGAGTTTTGGATTAGAGGGTTTG 60.379 45.833 0.00 0.00 0.00 2.93
750 4518 5.001232 CGAGTTTTGGATTAGAGGGTTTGA 58.999 41.667 0.00 0.00 0.00 2.69
751 4519 5.472137 CGAGTTTTGGATTAGAGGGTTTGAA 59.528 40.000 0.00 0.00 0.00 2.69
752 4520 6.348540 CGAGTTTTGGATTAGAGGGTTTGAAG 60.349 42.308 0.00 0.00 0.00 3.02
753 4521 5.775195 AGTTTTGGATTAGAGGGTTTGAAGG 59.225 40.000 0.00 0.00 0.00 3.46
754 4522 5.592587 TTTGGATTAGAGGGTTTGAAGGA 57.407 39.130 0.00 0.00 0.00 3.36
755 4523 5.796502 TTGGATTAGAGGGTTTGAAGGAT 57.203 39.130 0.00 0.00 0.00 3.24
756 4524 6.901615 TTGGATTAGAGGGTTTGAAGGATA 57.098 37.500 0.00 0.00 0.00 2.59
757 4525 6.901615 TGGATTAGAGGGTTTGAAGGATAA 57.098 37.500 0.00 0.00 0.00 1.75
758 4526 7.465900 TGGATTAGAGGGTTTGAAGGATAAT 57.534 36.000 0.00 0.00 0.00 1.28
759 4527 8.575736 TGGATTAGAGGGTTTGAAGGATAATA 57.424 34.615 0.00 0.00 0.00 0.98
760 4528 9.009675 TGGATTAGAGGGTTTGAAGGATAATAA 57.990 33.333 0.00 0.00 0.00 1.40
761 4529 9.862149 GGATTAGAGGGTTTGAAGGATAATAAA 57.138 33.333 0.00 0.00 0.00 1.40
764 4532 7.588497 AGAGGGTTTGAAGGATAATAAATGC 57.412 36.000 0.00 0.00 0.00 3.56
765 4533 7.357471 AGAGGGTTTGAAGGATAATAAATGCT 58.643 34.615 0.00 0.00 0.00 3.79
766 4534 7.503902 AGAGGGTTTGAAGGATAATAAATGCTC 59.496 37.037 0.00 0.00 0.00 4.26
767 4535 7.125391 AGGGTTTGAAGGATAATAAATGCTCA 58.875 34.615 0.00 0.00 0.00 4.26
768 4536 7.786464 AGGGTTTGAAGGATAATAAATGCTCAT 59.214 33.333 0.00 0.00 0.00 2.90
769 4537 8.424133 GGGTTTGAAGGATAATAAATGCTCATT 58.576 33.333 0.00 0.00 0.00 2.57
787 4555 9.678260 ATGCTCATTAACTTGATTTTAGTCTCT 57.322 29.630 0.00 0.00 0.00 3.10
788 4556 9.507329 TGCTCATTAACTTGATTTTAGTCTCTT 57.493 29.630 0.00 0.00 0.00 2.85
806 4574 8.499403 AGTCTCTTTAGTATTTGAATCCAAGC 57.501 34.615 0.00 0.00 33.23 4.01
807 4575 8.103305 AGTCTCTTTAGTATTTGAATCCAAGCA 58.897 33.333 0.00 0.00 33.23 3.91
808 4576 8.897752 GTCTCTTTAGTATTTGAATCCAAGCAT 58.102 33.333 0.00 0.00 33.23 3.79
809 4577 8.896744 TCTCTTTAGTATTTGAATCCAAGCATG 58.103 33.333 0.00 0.00 33.23 4.06
821 4589 1.236628 CAAGCATGGATGAGGCTAGC 58.763 55.000 6.04 6.04 42.15 3.42
822 4590 0.841961 AAGCATGGATGAGGCTAGCA 59.158 50.000 18.24 0.00 42.15 3.49
823 4591 0.841961 AGCATGGATGAGGCTAGCAA 59.158 50.000 18.24 1.28 40.84 3.91
824 4592 1.202782 AGCATGGATGAGGCTAGCAAG 60.203 52.381 18.24 0.00 40.84 4.01
825 4593 1.476471 GCATGGATGAGGCTAGCAAGT 60.476 52.381 18.24 0.00 0.00 3.16
826 4594 2.928334 CATGGATGAGGCTAGCAAGTT 58.072 47.619 18.24 0.00 0.00 2.66
827 4595 3.285484 CATGGATGAGGCTAGCAAGTTT 58.715 45.455 18.24 0.00 0.00 2.66
828 4596 3.439857 TGGATGAGGCTAGCAAGTTTT 57.560 42.857 18.24 0.00 0.00 2.43
829 4597 4.568072 TGGATGAGGCTAGCAAGTTTTA 57.432 40.909 18.24 0.00 0.00 1.52
830 4598 4.517285 TGGATGAGGCTAGCAAGTTTTAG 58.483 43.478 18.24 0.00 0.00 1.85
831 4599 4.019321 TGGATGAGGCTAGCAAGTTTTAGT 60.019 41.667 18.24 0.00 0.00 2.24
832 4600 4.572795 GGATGAGGCTAGCAAGTTTTAGTC 59.427 45.833 18.24 1.74 0.00 2.59
833 4601 4.891992 TGAGGCTAGCAAGTTTTAGTCT 57.108 40.909 18.24 0.00 34.70 3.24
834 4602 4.822026 TGAGGCTAGCAAGTTTTAGTCTC 58.178 43.478 18.24 14.63 44.83 3.36
835 4603 4.822026 GAGGCTAGCAAGTTTTAGTCTCA 58.178 43.478 18.24 0.00 44.29 3.27
836 4604 4.570930 AGGCTAGCAAGTTTTAGTCTCAC 58.429 43.478 18.24 0.00 25.59 3.51
837 4605 4.284746 AGGCTAGCAAGTTTTAGTCTCACT 59.715 41.667 18.24 0.00 25.59 3.41
838 4606 5.480772 AGGCTAGCAAGTTTTAGTCTCACTA 59.519 40.000 18.24 0.00 25.59 2.74
839 4607 5.577554 GGCTAGCAAGTTTTAGTCTCACTAC 59.422 44.000 18.24 0.00 28.93 2.73
840 4608 6.391537 GCTAGCAAGTTTTAGTCTCACTACT 58.608 40.000 10.63 0.00 28.93 2.57
841 4609 6.869388 GCTAGCAAGTTTTAGTCTCACTACTT 59.131 38.462 10.63 0.00 28.93 2.24
842 4610 7.385478 GCTAGCAAGTTTTAGTCTCACTACTTT 59.615 37.037 10.63 0.00 28.93 2.66
843 4611 9.262358 CTAGCAAGTTTTAGTCTCACTACTTTT 57.738 33.333 0.00 0.00 28.93 2.27
845 4613 9.262358 AGCAAGTTTTAGTCTCACTACTTTTAG 57.738 33.333 0.00 0.00 28.93 1.85
846 4614 9.043079 GCAAGTTTTAGTCTCACTACTTTTAGT 57.957 33.333 0.00 0.00 39.30 2.24
853 4621 9.516546 TTAGTCTCACTACTTTTAGTCATGAGA 57.483 33.333 14.29 14.29 42.35 3.27
870 4638 7.634522 GTCATGAGACTAAAACATATCCAAGC 58.365 38.462 0.00 0.00 41.64 4.01
871 4639 7.280876 GTCATGAGACTAAAACATATCCAAGCA 59.719 37.037 0.00 0.00 41.64 3.91
872 4640 6.985188 TGAGACTAAAACATATCCAAGCAC 57.015 37.500 0.00 0.00 0.00 4.40
873 4641 5.880332 TGAGACTAAAACATATCCAAGCACC 59.120 40.000 0.00 0.00 0.00 5.01
874 4642 5.193679 AGACTAAAACATATCCAAGCACCC 58.806 41.667 0.00 0.00 0.00 4.61
875 4643 5.044846 AGACTAAAACATATCCAAGCACCCT 60.045 40.000 0.00 0.00 0.00 4.34
1166 5115 1.529152 TTTAGCGAGTCCTGCGACCA 61.529 55.000 0.00 0.00 40.12 4.02
1681 5663 1.066303 TCGCATGTTTGCCTTCGTTTT 59.934 42.857 0.00 0.00 46.57 2.43
1812 5795 3.181492 TGTTTGATGAAATGCGTGTGTGT 60.181 39.130 0.00 0.00 0.00 3.72
1870 5853 1.691215 CTGGCGCTTCTTCTTCTCGC 61.691 60.000 7.64 0.00 44.39 5.03
2865 6862 1.228154 GGCGGGAGTCTGGTTTGTT 60.228 57.895 0.00 0.00 0.00 2.83
3067 7065 2.289072 TGCTGCTGTAGAAGAACTGACC 60.289 50.000 0.00 0.00 0.00 4.02
3132 7130 2.682856 GGAATGGTGCGCTCTAATTTGA 59.317 45.455 9.73 0.00 0.00 2.69
3301 7299 6.464322 CCTTCCTTTCCTTTTATTTTGCAGGT 60.464 38.462 0.00 0.00 0.00 4.00
3511 7515 9.038803 TGTGACTACCGTATGATCGTATATATC 57.961 37.037 0.00 0.00 0.00 1.63
3539 7543 9.702726 GCTGAAAAGTAAAACAATTTTTCCTTC 57.297 29.630 6.20 0.00 38.25 3.46
3622 7626 5.747197 GCTTCGACGAATATGAAGGTCTTTA 59.253 40.000 11.30 0.00 39.54 1.85
3681 7685 7.815383 TGATATAGAAACACCATCAGGGATTT 58.185 34.615 0.00 0.00 41.15 2.17
3837 7843 2.760650 CTGAGTAGCCATGTGTACAGGA 59.239 50.000 0.00 0.00 0.00 3.86
3853 7859 4.414337 ACAGGAAAGGCATCAGTCTATC 57.586 45.455 0.00 0.00 0.00 2.08
3854 7860 3.776969 ACAGGAAAGGCATCAGTCTATCA 59.223 43.478 0.00 0.00 0.00 2.15
4031 8043 5.735285 TTGCATACATCCATTTCCAACAA 57.265 34.783 0.00 0.00 0.00 2.83
4080 8092 8.924511 AGATATGTTCCTTTTCTTCTCAACAA 57.075 30.769 0.00 0.00 0.00 2.83
4217 8229 2.119495 GGATGGAGCTTTCCCTGTCTA 58.881 52.381 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 2.607750 AGCCCACAGGTCATCCGT 60.608 61.111 0.00 0.00 39.05 4.69
111 118 1.275856 GCACCCAGCCAATGAAATTCA 59.724 47.619 0.00 0.00 31.22 2.57
420 4188 2.044650 CGTCGACCCACCCCTCTA 60.045 66.667 10.58 0.00 0.00 2.43
443 4211 1.599518 GTGTGCACAATCCGGGTGA 60.600 57.895 23.59 0.00 38.54 4.02
528 4296 0.393537 GGATCCAAGCACCCTCACAG 60.394 60.000 6.95 0.00 0.00 3.66
529 4297 1.133181 TGGATCCAAGCACCCTCACA 61.133 55.000 13.46 0.00 0.00 3.58
530 4298 0.038166 TTGGATCCAAGCACCCTCAC 59.962 55.000 23.63 0.00 0.00 3.51
531 4299 0.329261 CTTGGATCCAAGCACCCTCA 59.671 55.000 35.47 9.07 45.38 3.86
532 4300 3.181526 CTTGGATCCAAGCACCCTC 57.818 57.895 35.47 0.00 45.38 4.30
539 4307 8.669243 GACTAAAATAAGTCACTTGGATCCAAG 58.331 37.037 40.81 40.81 45.09 3.61
540 4308 8.383175 AGACTAAAATAAGTCACTTGGATCCAA 58.617 33.333 25.53 25.53 46.89 3.53
541 4309 7.824289 CAGACTAAAATAAGTCACTTGGATCCA 59.176 37.037 11.44 11.44 46.89 3.41
542 4310 8.041323 TCAGACTAAAATAAGTCACTTGGATCC 58.959 37.037 4.20 4.20 46.89 3.36
543 4311 8.874816 GTCAGACTAAAATAAGTCACTTGGATC 58.125 37.037 0.00 0.00 46.89 3.36
544 4312 8.598041 AGTCAGACTAAAATAAGTCACTTGGAT 58.402 33.333 0.00 0.00 46.89 3.41
545 4313 7.963532 AGTCAGACTAAAATAAGTCACTTGGA 58.036 34.615 0.00 0.00 46.89 3.53
546 4314 9.706691 TTAGTCAGACTAAAATAAGTCACTTGG 57.293 33.333 19.07 0.00 46.89 3.61
565 4333 9.308318 GCCTCTTAAGAGACTATTTTTAGTCAG 57.692 37.037 30.17 10.99 46.62 3.51
566 4334 9.036980 AGCCTCTTAAGAGACTATTTTTAGTCA 57.963 33.333 30.17 0.00 46.62 3.41
574 4342 9.839817 GGAATTTTAGCCTCTTAAGAGACTATT 57.160 33.333 30.17 20.44 44.74 1.73
575 4343 8.993424 TGGAATTTTAGCCTCTTAAGAGACTAT 58.007 33.333 30.17 15.00 44.74 2.12
576 4344 8.375493 TGGAATTTTAGCCTCTTAAGAGACTA 57.625 34.615 30.17 25.33 44.74 2.59
577 4345 7.259088 TGGAATTTTAGCCTCTTAAGAGACT 57.741 36.000 30.17 26.34 44.74 3.24
578 4346 7.414651 GCTTGGAATTTTAGCCTCTTAAGAGAC 60.415 40.741 30.17 20.99 44.74 3.36
579 4347 6.599638 GCTTGGAATTTTAGCCTCTTAAGAGA 59.400 38.462 30.17 12.24 44.74 3.10
580 4348 6.375455 TGCTTGGAATTTTAGCCTCTTAAGAG 59.625 38.462 23.31 23.31 41.71 2.85
581 4349 6.151144 GTGCTTGGAATTTTAGCCTCTTAAGA 59.849 38.462 4.81 4.81 34.03 2.10
582 4350 6.325596 GTGCTTGGAATTTTAGCCTCTTAAG 58.674 40.000 0.00 0.00 34.03 1.85
583 4351 5.185056 GGTGCTTGGAATTTTAGCCTCTTAA 59.815 40.000 0.00 0.00 34.03 1.85
584 4352 4.705023 GGTGCTTGGAATTTTAGCCTCTTA 59.295 41.667 0.00 0.00 34.03 2.10
585 4353 3.511540 GGTGCTTGGAATTTTAGCCTCTT 59.488 43.478 0.00 0.00 34.03 2.85
586 4354 3.092301 GGTGCTTGGAATTTTAGCCTCT 58.908 45.455 0.00 0.00 34.03 3.69
587 4355 2.166459 GGGTGCTTGGAATTTTAGCCTC 59.834 50.000 0.00 0.00 34.03 4.70
588 4356 2.179427 GGGTGCTTGGAATTTTAGCCT 58.821 47.619 0.00 0.00 34.03 4.58
589 4357 1.207089 GGGGTGCTTGGAATTTTAGCC 59.793 52.381 0.00 0.00 34.03 3.93
590 4358 2.094026 CAGGGGTGCTTGGAATTTTAGC 60.094 50.000 0.00 0.00 35.50 3.09
591 4359 3.193479 GTCAGGGGTGCTTGGAATTTTAG 59.807 47.826 0.00 0.00 0.00 1.85
592 4360 3.161866 GTCAGGGGTGCTTGGAATTTTA 58.838 45.455 0.00 0.00 0.00 1.52
593 4361 1.970640 GTCAGGGGTGCTTGGAATTTT 59.029 47.619 0.00 0.00 0.00 1.82
594 4362 1.147817 AGTCAGGGGTGCTTGGAATTT 59.852 47.619 0.00 0.00 0.00 1.82
595 4363 0.779997 AGTCAGGGGTGCTTGGAATT 59.220 50.000 0.00 0.00 0.00 2.17
596 4364 1.668826 TAGTCAGGGGTGCTTGGAAT 58.331 50.000 0.00 0.00 0.00 3.01
597 4365 1.440618 TTAGTCAGGGGTGCTTGGAA 58.559 50.000 0.00 0.00 0.00 3.53
598 4366 1.351017 CTTTAGTCAGGGGTGCTTGGA 59.649 52.381 0.00 0.00 0.00 3.53
599 4367 1.351017 TCTTTAGTCAGGGGTGCTTGG 59.649 52.381 0.00 0.00 0.00 3.61
600 4368 2.616510 CCTCTTTAGTCAGGGGTGCTTG 60.617 54.545 0.00 0.00 28.24 4.01
601 4369 1.630878 CCTCTTTAGTCAGGGGTGCTT 59.369 52.381 0.00 0.00 28.24 3.91
602 4370 1.280457 CCTCTTTAGTCAGGGGTGCT 58.720 55.000 0.00 0.00 28.24 4.40
603 4371 0.253327 CCCTCTTTAGTCAGGGGTGC 59.747 60.000 0.00 0.00 45.39 5.01
608 4376 4.019231 AGTTTTAGCCCCTCTTTAGTCAGG 60.019 45.833 0.00 0.00 0.00 3.86
609 4377 5.167303 AGTTTTAGCCCCTCTTTAGTCAG 57.833 43.478 0.00 0.00 0.00 3.51
610 4378 5.783875 ACTAGTTTTAGCCCCTCTTTAGTCA 59.216 40.000 0.00 0.00 0.00 3.41
611 4379 6.154877 AGACTAGTTTTAGCCCCTCTTTAGTC 59.845 42.308 0.00 0.00 36.42 2.59
612 4380 6.024247 AGACTAGTTTTAGCCCCTCTTTAGT 58.976 40.000 0.00 0.00 0.00 2.24
613 4381 6.547930 AGACTAGTTTTAGCCCCTCTTTAG 57.452 41.667 0.00 0.00 0.00 1.85
614 4382 5.126707 CGAGACTAGTTTTAGCCCCTCTTTA 59.873 44.000 0.00 0.00 0.00 1.85
615 4383 4.081586 CGAGACTAGTTTTAGCCCCTCTTT 60.082 45.833 0.00 0.00 0.00 2.52
616 4384 3.447944 CGAGACTAGTTTTAGCCCCTCTT 59.552 47.826 0.00 0.00 0.00 2.85
617 4385 3.025262 CGAGACTAGTTTTAGCCCCTCT 58.975 50.000 0.00 0.00 0.00 3.69
618 4386 3.022406 TCGAGACTAGTTTTAGCCCCTC 58.978 50.000 0.00 0.00 0.00 4.30
619 4387 3.025262 CTCGAGACTAGTTTTAGCCCCT 58.975 50.000 6.58 0.00 0.00 4.79
620 4388 3.022406 TCTCGAGACTAGTTTTAGCCCC 58.978 50.000 12.08 0.00 0.00 5.80
621 4389 4.031418 GTCTCGAGACTAGTTTTAGCCC 57.969 50.000 33.28 6.70 41.65 5.19
642 4410 6.402875 GGGTACCGCTGACTAAAACATTTTAG 60.403 42.308 18.37 18.37 46.31 1.85
643 4411 5.412286 GGGTACCGCTGACTAAAACATTTTA 59.588 40.000 5.65 0.00 40.86 1.52
644 4412 4.216902 GGGTACCGCTGACTAAAACATTTT 59.783 41.667 5.65 0.00 40.86 1.82
645 4413 3.754850 GGGTACCGCTGACTAAAACATTT 59.245 43.478 5.65 0.00 40.86 2.32
646 4414 3.340928 GGGTACCGCTGACTAAAACATT 58.659 45.455 5.65 0.00 40.86 2.71
647 4415 2.981898 GGGTACCGCTGACTAAAACAT 58.018 47.619 5.65 0.00 40.86 2.71
648 4416 2.460757 GGGTACCGCTGACTAAAACA 57.539 50.000 5.65 0.00 40.86 2.83
662 4430 9.281371 GACTAATCCACATTTTAATAGGGGTAC 57.719 37.037 0.00 0.00 0.00 3.34
663 4431 8.442374 GGACTAATCCACATTTTAATAGGGGTA 58.558 37.037 0.00 0.00 45.47 3.69
664 4432 7.295340 GGACTAATCCACATTTTAATAGGGGT 58.705 38.462 0.00 0.00 45.47 4.95
665 4433 7.761038 GGACTAATCCACATTTTAATAGGGG 57.239 40.000 0.00 0.00 45.47 4.79
680 4448 4.447138 TGAGGAGAGAGAGGACTAATCC 57.553 50.000 0.00 0.00 46.69 3.01
681 4449 6.976934 AAATGAGGAGAGAGAGGACTAATC 57.023 41.667 0.00 0.00 0.00 1.75
682 4450 9.445973 AATTAAATGAGGAGAGAGAGGACTAAT 57.554 33.333 0.00 0.00 0.00 1.73
683 4451 8.846423 AATTAAATGAGGAGAGAGAGGACTAA 57.154 34.615 0.00 0.00 0.00 2.24
684 4452 7.507616 GGAATTAAATGAGGAGAGAGAGGACTA 59.492 40.741 0.00 0.00 0.00 2.59
685 4453 6.326323 GGAATTAAATGAGGAGAGAGAGGACT 59.674 42.308 0.00 0.00 0.00 3.85
686 4454 6.326323 AGGAATTAAATGAGGAGAGAGAGGAC 59.674 42.308 0.00 0.00 0.00 3.85
687 4455 6.448202 AGGAATTAAATGAGGAGAGAGAGGA 58.552 40.000 0.00 0.00 0.00 3.71
688 4456 6.554605 AGAGGAATTAAATGAGGAGAGAGAGG 59.445 42.308 0.00 0.00 0.00 3.69
689 4457 7.601705 AGAGGAATTAAATGAGGAGAGAGAG 57.398 40.000 0.00 0.00 0.00 3.20
690 4458 7.843760 AGAAGAGGAATTAAATGAGGAGAGAGA 59.156 37.037 0.00 0.00 0.00 3.10
691 4459 8.021898 AGAAGAGGAATTAAATGAGGAGAGAG 57.978 38.462 0.00 0.00 0.00 3.20
692 4460 7.986553 AGAAGAGGAATTAAATGAGGAGAGA 57.013 36.000 0.00 0.00 0.00 3.10
701 4469 9.860898 GCATGTGTTAAAGAAGAGGAATTAAAT 57.139 29.630 0.00 0.00 0.00 1.40
702 4470 8.020819 CGCATGTGTTAAAGAAGAGGAATTAAA 58.979 33.333 0.00 0.00 0.00 1.52
703 4471 7.389330 TCGCATGTGTTAAAGAAGAGGAATTAA 59.611 33.333 6.09 0.00 0.00 1.40
704 4472 6.876789 TCGCATGTGTTAAAGAAGAGGAATTA 59.123 34.615 6.09 0.00 0.00 1.40
705 4473 5.705441 TCGCATGTGTTAAAGAAGAGGAATT 59.295 36.000 6.09 0.00 0.00 2.17
706 4474 5.245531 TCGCATGTGTTAAAGAAGAGGAAT 58.754 37.500 6.09 0.00 0.00 3.01
707 4475 4.637276 TCGCATGTGTTAAAGAAGAGGAA 58.363 39.130 6.09 0.00 0.00 3.36
708 4476 4.245660 CTCGCATGTGTTAAAGAAGAGGA 58.754 43.478 6.09 0.00 0.00 3.71
709 4477 3.997021 ACTCGCATGTGTTAAAGAAGAGG 59.003 43.478 6.09 0.00 0.00 3.69
710 4478 5.597813 AACTCGCATGTGTTAAAGAAGAG 57.402 39.130 6.09 0.00 30.46 2.85
711 4479 6.198687 CAAAACTCGCATGTGTTAAAGAAGA 58.801 36.000 6.09 0.00 31.90 2.87
712 4480 5.399301 CCAAAACTCGCATGTGTTAAAGAAG 59.601 40.000 6.09 0.00 31.90 2.85
713 4481 5.066634 TCCAAAACTCGCATGTGTTAAAGAA 59.933 36.000 6.09 0.00 31.90 2.52
714 4482 4.576873 TCCAAAACTCGCATGTGTTAAAGA 59.423 37.500 6.09 0.00 31.90 2.52
715 4483 4.854399 TCCAAAACTCGCATGTGTTAAAG 58.146 39.130 6.09 0.00 31.90 1.85
716 4484 4.902443 TCCAAAACTCGCATGTGTTAAA 57.098 36.364 6.09 0.00 31.90 1.52
717 4485 5.446143 AATCCAAAACTCGCATGTGTTAA 57.554 34.783 6.09 0.00 31.90 2.01
718 4486 5.935206 TCTAATCCAAAACTCGCATGTGTTA 59.065 36.000 6.09 0.00 31.90 2.41
719 4487 4.759693 TCTAATCCAAAACTCGCATGTGTT 59.240 37.500 6.09 0.82 33.46 3.32
720 4488 4.323417 TCTAATCCAAAACTCGCATGTGT 58.677 39.130 6.09 0.00 0.00 3.72
721 4489 4.201851 CCTCTAATCCAAAACTCGCATGTG 60.202 45.833 0.00 0.00 0.00 3.21
722 4490 3.941483 CCTCTAATCCAAAACTCGCATGT 59.059 43.478 0.00 0.00 0.00 3.21
723 4491 3.313526 CCCTCTAATCCAAAACTCGCATG 59.686 47.826 0.00 0.00 0.00 4.06
724 4492 3.054361 ACCCTCTAATCCAAAACTCGCAT 60.054 43.478 0.00 0.00 0.00 4.73
725 4493 2.304761 ACCCTCTAATCCAAAACTCGCA 59.695 45.455 0.00 0.00 0.00 5.10
726 4494 2.987232 ACCCTCTAATCCAAAACTCGC 58.013 47.619 0.00 0.00 0.00 5.03
727 4495 5.001232 TCAAACCCTCTAATCCAAAACTCG 58.999 41.667 0.00 0.00 0.00 4.18
728 4496 6.071896 CCTTCAAACCCTCTAATCCAAAACTC 60.072 42.308 0.00 0.00 0.00 3.01
729 4497 5.775195 CCTTCAAACCCTCTAATCCAAAACT 59.225 40.000 0.00 0.00 0.00 2.66
730 4498 5.773176 TCCTTCAAACCCTCTAATCCAAAAC 59.227 40.000 0.00 0.00 0.00 2.43
731 4499 5.959512 TCCTTCAAACCCTCTAATCCAAAA 58.040 37.500 0.00 0.00 0.00 2.44
732 4500 5.592587 TCCTTCAAACCCTCTAATCCAAA 57.407 39.130 0.00 0.00 0.00 3.28
733 4501 5.796502 ATCCTTCAAACCCTCTAATCCAA 57.203 39.130 0.00 0.00 0.00 3.53
734 4502 6.901615 TTATCCTTCAAACCCTCTAATCCA 57.098 37.500 0.00 0.00 0.00 3.41
735 4503 9.862149 TTTATTATCCTTCAAACCCTCTAATCC 57.138 33.333 0.00 0.00 0.00 3.01
738 4506 9.131791 GCATTTATTATCCTTCAAACCCTCTAA 57.868 33.333 0.00 0.00 0.00 2.10
739 4507 8.502738 AGCATTTATTATCCTTCAAACCCTCTA 58.497 33.333 0.00 0.00 0.00 2.43
740 4508 7.357471 AGCATTTATTATCCTTCAAACCCTCT 58.643 34.615 0.00 0.00 0.00 3.69
741 4509 7.285401 TGAGCATTTATTATCCTTCAAACCCTC 59.715 37.037 0.00 0.00 0.00 4.30
742 4510 7.125391 TGAGCATTTATTATCCTTCAAACCCT 58.875 34.615 0.00 0.00 0.00 4.34
743 4511 7.346751 TGAGCATTTATTATCCTTCAAACCC 57.653 36.000 0.00 0.00 0.00 4.11
761 4529 9.678260 AGAGACTAAAATCAAGTTAATGAGCAT 57.322 29.630 0.00 0.00 31.76 3.79
762 4530 9.507329 AAGAGACTAAAATCAAGTTAATGAGCA 57.493 29.630 0.00 0.00 31.76 4.26
780 4548 9.601217 GCTTGGATTCAAATACTAAAGAGACTA 57.399 33.333 0.00 0.00 31.77 2.59
781 4549 8.103305 TGCTTGGATTCAAATACTAAAGAGACT 58.897 33.333 0.00 0.00 31.77 3.24
782 4550 8.268850 TGCTTGGATTCAAATACTAAAGAGAC 57.731 34.615 0.00 0.00 31.77 3.36
783 4551 8.896744 CATGCTTGGATTCAAATACTAAAGAGA 58.103 33.333 0.00 0.00 31.77 3.10
784 4552 8.133627 CCATGCTTGGATTCAAATACTAAAGAG 58.866 37.037 13.33 0.00 46.92 2.85
785 4553 7.999679 CCATGCTTGGATTCAAATACTAAAGA 58.000 34.615 13.33 0.00 46.92 2.52
801 4569 1.893544 CTAGCCTCATCCATGCTTGG 58.106 55.000 12.41 12.41 45.15 3.61
802 4570 1.236628 GCTAGCCTCATCCATGCTTG 58.763 55.000 2.29 0.00 36.57 4.01
803 4571 0.841961 TGCTAGCCTCATCCATGCTT 59.158 50.000 13.29 0.00 36.57 3.91
804 4572 0.841961 TTGCTAGCCTCATCCATGCT 59.158 50.000 13.29 0.00 39.10 3.79
805 4573 1.236628 CTTGCTAGCCTCATCCATGC 58.763 55.000 13.29 0.00 0.00 4.06
806 4574 2.634815 ACTTGCTAGCCTCATCCATG 57.365 50.000 13.29 0.00 0.00 3.66
807 4575 3.659183 AAACTTGCTAGCCTCATCCAT 57.341 42.857 13.29 0.00 0.00 3.41
808 4576 3.439857 AAAACTTGCTAGCCTCATCCA 57.560 42.857 13.29 0.00 0.00 3.41
809 4577 4.518249 ACTAAAACTTGCTAGCCTCATCC 58.482 43.478 13.29 0.00 0.00 3.51
810 4578 5.423886 AGACTAAAACTTGCTAGCCTCATC 58.576 41.667 13.29 0.00 0.00 2.92
811 4579 5.046304 TGAGACTAAAACTTGCTAGCCTCAT 60.046 40.000 13.29 0.00 31.94 2.90
812 4580 4.283467 TGAGACTAAAACTTGCTAGCCTCA 59.717 41.667 13.29 10.30 33.75 3.86
813 4581 4.627900 GTGAGACTAAAACTTGCTAGCCTC 59.372 45.833 13.29 7.74 0.00 4.70
814 4582 4.284746 AGTGAGACTAAAACTTGCTAGCCT 59.715 41.667 13.29 0.00 0.00 4.58
815 4583 4.570930 AGTGAGACTAAAACTTGCTAGCC 58.429 43.478 13.29 0.00 0.00 3.93
816 4584 6.391537 AGTAGTGAGACTAAAACTTGCTAGC 58.608 40.000 8.10 8.10 31.62 3.42
817 4585 8.819643 AAAGTAGTGAGACTAAAACTTGCTAG 57.180 34.615 0.00 0.00 31.62 3.42
819 4587 9.262358 CTAAAAGTAGTGAGACTAAAACTTGCT 57.738 33.333 0.00 0.00 31.62 3.91
820 4588 9.043079 ACTAAAAGTAGTGAGACTAAAACTTGC 57.957 33.333 0.00 0.00 39.20 4.01
827 4595 9.516546 TCTCATGACTAAAAGTAGTGAGACTAA 57.483 33.333 14.80 0.96 40.65 2.24
845 4613 7.280876 TGCTTGGATATGTTTTAGTCTCATGAC 59.719 37.037 0.00 0.00 43.22 3.06
846 4614 7.280876 GTGCTTGGATATGTTTTAGTCTCATGA 59.719 37.037 0.00 0.00 0.00 3.07
847 4615 7.412853 GTGCTTGGATATGTTTTAGTCTCATG 58.587 38.462 0.00 0.00 0.00 3.07
848 4616 6.543831 GGTGCTTGGATATGTTTTAGTCTCAT 59.456 38.462 0.00 0.00 0.00 2.90
849 4617 5.880332 GGTGCTTGGATATGTTTTAGTCTCA 59.120 40.000 0.00 0.00 0.00 3.27
850 4618 5.297029 GGGTGCTTGGATATGTTTTAGTCTC 59.703 44.000 0.00 0.00 0.00 3.36
851 4619 5.044846 AGGGTGCTTGGATATGTTTTAGTCT 60.045 40.000 0.00 0.00 0.00 3.24
852 4620 5.193679 AGGGTGCTTGGATATGTTTTAGTC 58.806 41.667 0.00 0.00 0.00 2.59
853 4621 5.044846 AGAGGGTGCTTGGATATGTTTTAGT 60.045 40.000 0.00 0.00 0.00 2.24
854 4622 5.297776 CAGAGGGTGCTTGGATATGTTTTAG 59.702 44.000 0.00 0.00 0.00 1.85
855 4623 5.192927 CAGAGGGTGCTTGGATATGTTTTA 58.807 41.667 0.00 0.00 0.00 1.52
856 4624 4.019174 CAGAGGGTGCTTGGATATGTTTT 58.981 43.478 0.00 0.00 0.00 2.43
857 4625 3.010584 ACAGAGGGTGCTTGGATATGTTT 59.989 43.478 0.00 0.00 0.00 2.83
858 4626 2.578021 ACAGAGGGTGCTTGGATATGTT 59.422 45.455 0.00 0.00 0.00 2.71
859 4627 2.092753 CACAGAGGGTGCTTGGATATGT 60.093 50.000 0.00 0.00 41.36 2.29
860 4628 2.569059 CACAGAGGGTGCTTGGATATG 58.431 52.381 0.00 0.00 41.36 1.78
871 4639 1.878656 GCGCACTAGACACAGAGGGT 61.879 60.000 0.30 0.00 0.00 4.34
872 4640 1.153745 GCGCACTAGACACAGAGGG 60.154 63.158 0.30 0.00 0.00 4.30
873 4641 1.515088 CGCGCACTAGACACAGAGG 60.515 63.158 8.75 0.00 0.00 3.69
874 4642 1.067743 CACGCGCACTAGACACAGAG 61.068 60.000 5.73 0.00 0.00 3.35
875 4643 1.081442 CACGCGCACTAGACACAGA 60.081 57.895 5.73 0.00 0.00 3.41
1219 5168 1.887242 GACACAGCTTGTCGTGGCA 60.887 57.895 11.53 0.00 45.33 4.92
1505 5479 0.721718 GCACGGCGAGGCAATATATC 59.278 55.000 16.62 0.00 0.00 1.63
1681 5663 2.790433 GTACCAAACTGCCCATGAAGA 58.210 47.619 0.00 0.00 0.00 2.87
1812 5795 2.129607 GAACCGTAGAACAAGCGTCAA 58.870 47.619 0.00 0.00 0.00 3.18
1870 5853 2.125106 GGTAAGCAGCAGGACCGG 60.125 66.667 0.00 0.00 0.00 5.28
2385 6378 1.750399 GCGCACCTGATTCCACCAT 60.750 57.895 0.30 0.00 0.00 3.55
2745 6742 8.514594 TCATTTCTAAAATAGAAGTGCACCAAG 58.485 33.333 14.63 0.00 46.17 3.61
3059 7057 5.423015 ACTACACATCATGATGGTCAGTTC 58.577 41.667 33.31 0.00 42.91 3.01
3132 7130 7.554835 TGCGAATACATTAGGAAATACCACTTT 59.445 33.333 0.00 0.00 42.04 2.66
3301 7299 4.441634 GGAGCAACCTTAGCGATTCTAGAA 60.442 45.833 7.82 7.82 37.01 2.10
3511 7515 8.882736 AGGAAAAATTGTTTTACTTTTCAGCAG 58.117 29.630 8.03 0.00 44.15 4.24
3528 7532 5.560966 ATGTATCGTGCGAAGGAAAAATT 57.439 34.783 0.00 0.00 0.00 1.82
3539 7543 7.783209 TCTCATTACAAATTATGTATCGTGCG 58.217 34.615 2.66 0.00 43.84 5.34
3622 7626 5.594317 GGAATAAAGGAGTGTATGCCAACAT 59.406 40.000 0.00 0.00 40.49 2.71
4031 8043 6.819947 AATTTATACGGACTCCCCTAGTTT 57.180 37.500 0.00 0.00 39.07 2.66
4211 8223 6.369065 GGTAGAACATTCAACAAGGTAGACAG 59.631 42.308 0.00 0.00 0.00 3.51
4217 8229 4.766891 CCATGGTAGAACATTCAACAAGGT 59.233 41.667 2.57 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.