Multiple sequence alignment - TraesCS4A01G333300

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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 TraesCS4A01G333300 chr4A 100.000 2465 0 0 1 2465 616978749 616976285 0.000000e+00 4553.0
1 TraesCS4A01G333300 chr4A 83.932 946 81 41 700 1590 616962120 616961191 0.000000e+00 839.0
2 TraesCS4A01G333300 chr5B 87.927 1433 86 32 663 2048 703268418 703269810 0.000000e+00 1607.0
3 TraesCS4A01G333300 chr5B 84.030 1052 75 47 700 1709 703291351 703292351 0.000000e+00 926.0
4 TraesCS4A01G333300 chr5B 85.115 786 65 24 1695 2465 703299570 703300318 0.000000e+00 756.0
5 TraesCS4A01G333300 chr5B 83.095 769 74 32 831 1580 703271395 703272126 0.000000e+00 649.0
6 TraesCS4A01G333300 chr5B 81.784 807 66 44 700 1466 703305588 703306353 3.510000e-168 601.0
7 TraesCS4A01G333300 chr5B 84.739 249 11 6 268 496 703265342 703265583 8.870000e-55 224.0
8 TraesCS4A01G333300 chr5B 90.909 55 3 2 617 670 447051023 447050970 3.400000e-09 73.1
9 TraesCS4A01G333300 chr5B 87.500 64 6 2 192 255 522942355 522942294 3.400000e-09 73.1
10 TraesCS4A01G333300 chr5D 87.196 1109 59 30 681 1724 550646087 550647177 0.000000e+00 1184.0
11 TraesCS4A01G333300 chr5D 91.350 763 38 11 949 1686 550965474 550966233 0.000000e+00 1018.0
12 TraesCS4A01G333300 chr5D 86.294 715 72 14 1761 2465 550966534 550967232 0.000000e+00 754.0
13 TraesCS4A01G333300 chr5D 84.769 650 56 24 828 1443 550964560 550965200 1.620000e-171 612.0
14 TraesCS4A01G333300 chr5D 86.239 545 37 16 271 799 550956983 550957505 7.700000e-155 556.0
15 TraesCS4A01G333300 chr5D 80.424 802 68 56 700 1466 551024361 551025108 1.680000e-146 529.0
16 TraesCS4A01G333300 chr5D 92.245 245 11 3 363 603 550645817 550646057 8.440000e-90 340.0
17 TraesCS4A01G333300 chr5D 87.459 303 28 8 1255 1553 550661170 550661466 8.440000e-90 340.0
18 TraesCS4A01G333300 chr5D 88.021 192 16 3 1392 1580 550985390 550985577 1.150000e-53 220.0
19 TraesCS4A01G333300 chr5D 88.750 160 8 5 788 946 550965212 550965362 1.160000e-43 187.0
20 TraesCS4A01G333300 chr5D 79.487 234 18 17 705 923 550660217 550660435 3.310000e-29 139.0
21 TraesCS4A01G333300 chr5D 91.071 56 3 2 616 670 9557611 9557557 9.450000e-10 75.0
22 TraesCS4A01G333300 chr2A 87.755 343 38 4 2035 2375 674201980 674201640 4.940000e-107 398.0
23 TraesCS4A01G333300 chr3A 84.127 378 55 4 2002 2375 648374068 648373692 6.480000e-96 361.0
24 TraesCS4A01G333300 chr3A 88.679 53 5 1 615 667 265252200 265252149 2.050000e-06 63.9
25 TraesCS4A01G333300 chr2D 85.672 335 46 2 2042 2375 529614628 529614295 3.900000e-93 351.0
26 TraesCS4A01G333300 chr2D 83.954 349 53 3 2002 2347 117476488 117476140 5.080000e-87 331.0
27 TraesCS4A01G333300 chr2D 87.037 54 3 4 615 667 11779621 11779571 9.520000e-05 58.4
28 TraesCS4A01G333300 chr1D 83.467 375 56 5 2002 2374 370101847 370101477 6.530000e-91 344.0
29 TraesCS4A01G333300 chr1D 82.456 342 58 2 2002 2342 234010838 234010498 5.150000e-77 298.0
30 TraesCS4A01G333300 chr5A 85.119 336 48 2 2042 2375 361904789 361905124 2.350000e-90 342.0
31 TraesCS4A01G333300 chr5A 85.714 56 7 1 612 666 476428977 476429032 9.520000e-05 58.4
32 TraesCS4A01G333300 chr3D 95.312 64 3 0 84 147 295150787 295150850 4.340000e-18 102.0
33 TraesCS4A01G333300 chr1A 86.458 96 10 2 1720 1815 7230276 7230184 4.340000e-18 102.0
34 TraesCS4A01G333300 chr7D 78.000 150 23 8 1721 1864 80766939 80767084 4.370000e-13 86.1
35 TraesCS4A01G333300 chr7B 77.632 152 27 4 1722 1866 586931813 586931964 4.370000e-13 86.1
36 TraesCS4A01G333300 chr7B 87.037 54 2 4 1053 1105 635138377 635138426 3.420000e-04 56.5
37 TraesCS4A01G333300 chr7A 89.231 65 4 3 192 255 540060013 540059951 7.310000e-11 78.7
38 TraesCS4A01G333300 chr7A 89.231 65 4 3 192 255 540105533 540105471 7.310000e-11 78.7
39 TraesCS4A01G333300 chr6D 88.333 60 3 4 614 670 44425862 44425920 4.400000e-08 69.4
40 TraesCS4A01G333300 chr6A 88.679 53 2 3 615 666 522945272 522945223 7.360000e-06 62.1
41 TraesCS4A01G333300 chr4B 88.462 52 4 2 615 666 605115175 605115126 7.360000e-06 62.1
42 TraesCS4A01G333300 chr6B 92.308 39 2 1 1837 1874 496991877 496991839 1.000000e-03 54.7


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 TraesCS4A01G333300 chr4A 616976285 616978749 2464 True 4553.000000 4553 100.000000 1 2465 1 chr4A.!!$R2 2464
1 TraesCS4A01G333300 chr4A 616961191 616962120 929 True 839.000000 839 83.932000 700 1590 1 chr4A.!!$R1 890
2 TraesCS4A01G333300 chr5B 703291351 703292351 1000 False 926.000000 926 84.030000 700 1709 1 chr5B.!!$F1 1009
3 TraesCS4A01G333300 chr5B 703265342 703272126 6784 False 826.666667 1607 85.253667 268 2048 3 chr5B.!!$F4 1780
4 TraesCS4A01G333300 chr5B 703299570 703300318 748 False 756.000000 756 85.115000 1695 2465 1 chr5B.!!$F2 770
5 TraesCS4A01G333300 chr5B 703305588 703306353 765 False 601.000000 601 81.784000 700 1466 1 chr5B.!!$F3 766
6 TraesCS4A01G333300 chr5D 550645817 550647177 1360 False 762.000000 1184 89.720500 363 1724 2 chr5D.!!$F4 1361
7 TraesCS4A01G333300 chr5D 550964560 550967232 2672 False 642.750000 1018 87.790750 788 2465 4 chr5D.!!$F6 1677
8 TraesCS4A01G333300 chr5D 550956983 550957505 522 False 556.000000 556 86.239000 271 799 1 chr5D.!!$F1 528
9 TraesCS4A01G333300 chr5D 551024361 551025108 747 False 529.000000 529 80.424000 700 1466 1 chr5D.!!$F3 766
10 TraesCS4A01G333300 chr5D 550660217 550661466 1249 False 239.500000 340 83.473000 705 1553 2 chr5D.!!$F5 848

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
36 37 0.040692 TCATATACACGTCGAGCGGC 60.041 55.0 0.0 0.0 46.52 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 5543 1.411394 TTAAGTTTCGCTCGTCGTGG 58.589 50.0 0.0 0.0 39.67 4.94 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
17 18 3.234349 CTCTGCCGGTCCATCCAT 58.766 61.111 1.90 0.00 35.57 3.41
18 19 1.070445 CTCTGCCGGTCCATCCATC 59.930 63.158 1.90 0.00 35.57 3.51
19 20 1.688884 TCTGCCGGTCCATCCATCA 60.689 57.895 1.90 0.00 35.57 3.07
20 21 1.056125 TCTGCCGGTCCATCCATCAT 61.056 55.000 1.90 0.00 35.57 2.45
21 22 0.686789 CTGCCGGTCCATCCATCATA 59.313 55.000 1.90 0.00 35.57 2.15
22 23 1.280133 CTGCCGGTCCATCCATCATAT 59.720 52.381 1.90 0.00 35.57 1.78
23 24 2.501316 CTGCCGGTCCATCCATCATATA 59.499 50.000 1.90 0.00 35.57 0.86
24 25 2.236146 TGCCGGTCCATCCATCATATAC 59.764 50.000 1.90 0.00 35.57 1.47
25 26 2.236146 GCCGGTCCATCCATCATATACA 59.764 50.000 1.90 0.00 35.57 2.29
26 27 3.861840 CCGGTCCATCCATCATATACAC 58.138 50.000 0.00 0.00 35.57 2.90
27 28 3.511699 CGGTCCATCCATCATATACACG 58.488 50.000 0.00 0.00 35.57 4.49
28 29 3.056821 CGGTCCATCCATCATATACACGT 60.057 47.826 0.00 0.00 35.57 4.49
29 30 4.495422 GGTCCATCCATCATATACACGTC 58.505 47.826 0.00 0.00 35.97 4.34
30 31 4.166523 GTCCATCCATCATATACACGTCG 58.833 47.826 0.00 0.00 0.00 5.12
31 32 4.076394 TCCATCCATCATATACACGTCGA 58.924 43.478 0.00 0.00 0.00 4.20
32 33 4.156008 TCCATCCATCATATACACGTCGAG 59.844 45.833 0.00 0.00 0.00 4.04
33 34 3.554259 TCCATCATATACACGTCGAGC 57.446 47.619 0.00 0.00 0.00 5.03
35 36 2.242564 CATCATATACACGTCGAGCGG 58.757 52.381 0.00 4.22 46.52 5.52
36 37 0.040692 TCATATACACGTCGAGCGGC 60.041 55.000 0.00 0.00 46.52 6.53
37 38 1.002250 CATATACACGTCGAGCGGCC 61.002 60.000 0.00 0.00 46.52 6.13
38 39 1.449726 ATATACACGTCGAGCGGCCA 61.450 55.000 2.24 0.00 46.52 5.36
39 40 2.055310 TATACACGTCGAGCGGCCAG 62.055 60.000 2.24 0.00 46.52 4.85
56 57 2.438434 GCGGCCAGCCAGTGTTAT 60.438 61.111 9.78 0.00 40.81 1.89
57 58 2.046285 GCGGCCAGCCAGTGTTATT 61.046 57.895 9.78 0.00 40.81 1.40
58 59 0.746563 GCGGCCAGCCAGTGTTATTA 60.747 55.000 9.78 0.00 40.81 0.98
59 60 1.967319 CGGCCAGCCAGTGTTATTAT 58.033 50.000 9.78 0.00 35.37 1.28
60 61 2.808933 GCGGCCAGCCAGTGTTATTATA 60.809 50.000 9.78 0.00 40.81 0.98
61 62 3.472652 CGGCCAGCCAGTGTTATTATAA 58.527 45.455 9.78 0.00 35.37 0.98
62 63 4.072131 CGGCCAGCCAGTGTTATTATAAT 58.928 43.478 9.78 2.97 35.37 1.28
63 64 4.518970 CGGCCAGCCAGTGTTATTATAATT 59.481 41.667 9.78 0.00 35.37 1.40
64 65 5.703592 CGGCCAGCCAGTGTTATTATAATTA 59.296 40.000 9.78 0.00 35.37 1.40
65 66 6.374333 CGGCCAGCCAGTGTTATTATAATTAT 59.626 38.462 9.78 2.97 35.37 1.28
66 67 7.414098 CGGCCAGCCAGTGTTATTATAATTATC 60.414 40.741 9.78 0.00 35.37 1.75
67 68 7.393234 GGCCAGCCAGTGTTATTATAATTATCA 59.607 37.037 3.12 0.00 35.81 2.15
68 69 8.237267 GCCAGCCAGTGTTATTATAATTATCAC 58.763 37.037 2.68 10.29 0.00 3.06
69 70 9.507329 CCAGCCAGTGTTATTATAATTATCACT 57.493 33.333 16.74 16.74 35.49 3.41
113 114 9.901172 ACTCCATTCGTTCCTAAATATAAGTTT 57.099 29.630 0.00 0.00 0.00 2.66
145 146 8.353684 AGAGATTTCAATAGACACTACATACGG 58.646 37.037 0.00 0.00 0.00 4.02
146 147 8.234136 AGATTTCAATAGACACTACATACGGA 57.766 34.615 0.00 0.00 0.00 4.69
147 148 8.861086 AGATTTCAATAGACACTACATACGGAT 58.139 33.333 0.00 0.00 0.00 4.18
180 181 9.890629 AGTCATATTTTAGAGCACAGATTTACA 57.109 29.630 0.00 0.00 0.00 2.41
181 182 9.922305 GTCATATTTTAGAGCACAGATTTACAC 57.078 33.333 0.00 0.00 0.00 2.90
182 183 9.665719 TCATATTTTAGAGCACAGATTTACACA 57.334 29.630 0.00 0.00 0.00 3.72
187 188 9.462174 TTTTAGAGCACAGATTTACACATTTTG 57.538 29.630 0.00 0.00 0.00 2.44
188 189 5.464168 AGAGCACAGATTTACACATTTTGC 58.536 37.500 0.00 0.00 0.00 3.68
189 190 5.242393 AGAGCACAGATTTACACATTTTGCT 59.758 36.000 0.00 0.00 40.40 3.91
190 191 5.846203 AGCACAGATTTACACATTTTGCTT 58.154 33.333 0.00 0.00 34.15 3.91
191 192 5.922544 AGCACAGATTTACACATTTTGCTTC 59.077 36.000 0.00 0.00 34.15 3.86
192 193 5.164158 GCACAGATTTACACATTTTGCTTCG 60.164 40.000 0.00 0.00 0.00 3.79
193 194 5.914635 CACAGATTTACACATTTTGCTTCGT 59.085 36.000 0.00 0.00 0.00 3.85
194 195 7.075121 CACAGATTTACACATTTTGCTTCGTA 58.925 34.615 0.00 0.00 0.00 3.43
195 196 7.750458 CACAGATTTACACATTTTGCTTCGTAT 59.250 33.333 0.00 0.00 0.00 3.06
196 197 7.750458 ACAGATTTACACATTTTGCTTCGTATG 59.250 33.333 0.00 0.00 0.00 2.39
197 198 7.750458 CAGATTTACACATTTTGCTTCGTATGT 59.250 33.333 0.00 0.00 0.00 2.29
198 199 8.941977 AGATTTACACATTTTGCTTCGTATGTA 58.058 29.630 0.00 0.00 30.53 2.29
199 200 9.210426 GATTTACACATTTTGCTTCGTATGTAG 57.790 33.333 0.00 0.00 30.53 2.74
200 201 7.661127 TTACACATTTTGCTTCGTATGTAGT 57.339 32.000 0.00 0.00 30.53 2.73
201 202 6.165659 ACACATTTTGCTTCGTATGTAGTC 57.834 37.500 0.00 0.00 30.53 2.59
202 203 5.932303 ACACATTTTGCTTCGTATGTAGTCT 59.068 36.000 0.00 0.00 30.53 3.24
203 204 6.426937 ACACATTTTGCTTCGTATGTAGTCTT 59.573 34.615 0.00 0.00 30.53 3.01
204 205 7.041372 ACACATTTTGCTTCGTATGTAGTCTTT 60.041 33.333 0.00 0.00 30.53 2.52
205 206 7.803189 CACATTTTGCTTCGTATGTAGTCTTTT 59.197 33.333 0.00 0.00 30.53 2.27
206 207 8.349983 ACATTTTGCTTCGTATGTAGTCTTTTT 58.650 29.630 0.00 0.00 29.93 1.94
256 257 8.618240 TTTAGAAATGGAGGGAGTATTAGTCA 57.382 34.615 1.13 0.00 0.00 3.41
257 258 6.487299 AGAAATGGAGGGAGTATTAGTCAC 57.513 41.667 1.13 0.00 0.00 3.67
258 259 6.206042 AGAAATGGAGGGAGTATTAGTCACT 58.794 40.000 2.82 2.82 33.05 3.41
259 260 5.878406 AATGGAGGGAGTATTAGTCACTG 57.122 43.478 8.04 0.00 29.82 3.66
260 261 3.031736 TGGAGGGAGTATTAGTCACTGC 58.968 50.000 13.73 13.73 39.54 4.40
262 263 2.912690 GGGAGTATTAGTCACTGCCC 57.087 55.000 1.90 0.00 45.89 5.36
263 264 1.416772 GGGAGTATTAGTCACTGCCCC 59.583 57.143 1.90 0.00 45.89 5.80
264 265 1.068741 GGAGTATTAGTCACTGCCCCG 59.931 57.143 1.13 0.00 0.00 5.73
265 266 0.464452 AGTATTAGTCACTGCCCCGC 59.536 55.000 0.00 0.00 0.00 6.13
266 267 0.177141 GTATTAGTCACTGCCCCGCA 59.823 55.000 0.00 0.00 36.92 5.69
287 288 5.508872 GCAACGACTCTACGTATGAGTTAT 58.491 41.667 20.99 13.41 45.83 1.89
322 323 2.120355 TACACGTCGAGCTTCACGCA 62.120 55.000 16.02 2.20 42.61 5.24
333 334 2.420022 AGCTTCACGCACCAAATATGTC 59.580 45.455 0.00 0.00 42.61 3.06
334 335 2.787723 GCTTCACGCACCAAATATGTCG 60.788 50.000 0.00 0.00 38.92 4.35
370 386 9.334693 CAAAGTTGCAGTTAAGATTAATCTGAC 57.665 33.333 18.61 18.26 37.19 3.51
400 423 3.457749 AGAGGGACTTGGGAGATTTGATC 59.542 47.826 0.00 0.00 41.55 2.92
401 424 3.457749 GAGGGACTTGGGAGATTTGATCT 59.542 47.826 0.00 0.00 41.55 2.75
402 425 3.854994 AGGGACTTGGGAGATTTGATCTT 59.145 43.478 0.00 0.00 35.19 2.40
403 426 4.293368 AGGGACTTGGGAGATTTGATCTTT 59.707 41.667 0.00 0.00 35.19 2.52
404 427 4.400567 GGGACTTGGGAGATTTGATCTTTG 59.599 45.833 0.00 0.00 40.38 2.77
405 428 5.256474 GGACTTGGGAGATTTGATCTTTGA 58.744 41.667 0.00 0.00 40.38 2.69
406 429 5.890419 GGACTTGGGAGATTTGATCTTTGAT 59.110 40.000 0.00 0.00 40.38 2.57
435 458 1.579084 GGTGCGCGGTCCAATTGTAA 61.579 55.000 8.83 0.00 0.00 2.41
496 524 2.224784 CACCTTTGCCACCTTTACGTAC 59.775 50.000 0.00 0.00 0.00 3.67
498 526 3.143728 CCTTTGCCACCTTTACGTACTT 58.856 45.455 0.00 0.00 0.00 2.24
499 527 3.187842 CCTTTGCCACCTTTACGTACTTC 59.812 47.826 0.00 0.00 0.00 3.01
500 528 3.472283 TTGCCACCTTTACGTACTTCA 57.528 42.857 0.00 0.00 0.00 3.02
501 529 3.472283 TGCCACCTTTACGTACTTCAA 57.528 42.857 0.00 0.00 0.00 2.69
502 530 3.806380 TGCCACCTTTACGTACTTCAAA 58.194 40.909 0.00 0.00 0.00 2.69
504 532 4.214545 TGCCACCTTTACGTACTTCAAATG 59.785 41.667 0.00 0.00 0.00 2.32
505 533 4.214758 GCCACCTTTACGTACTTCAAATGT 59.785 41.667 0.00 0.00 0.00 2.71
506 534 5.278120 GCCACCTTTACGTACTTCAAATGTT 60.278 40.000 0.00 0.00 0.00 2.71
507 535 6.731164 CCACCTTTACGTACTTCAAATGTTT 58.269 36.000 0.00 0.00 0.00 2.83
508 536 6.854381 CCACCTTTACGTACTTCAAATGTTTC 59.146 38.462 0.00 0.00 0.00 2.78
509 537 6.854381 CACCTTTACGTACTTCAAATGTTTCC 59.146 38.462 0.00 0.00 0.00 3.13
569 3317 3.888930 ACATCCTTTTGTCCAACGTTCAT 59.111 39.130 0.00 0.00 0.00 2.57
592 3344 9.685276 TCATTTGTAATTCAACTCATGTAGGAT 57.315 29.630 0.00 0.00 35.61 3.24
655 3411 2.192443 CCCTGGCCTCTGCATCAG 59.808 66.667 3.32 0.00 40.13 2.90
656 3412 2.372890 CCCTGGCCTCTGCATCAGA 61.373 63.158 3.32 0.00 38.25 3.27
657 3413 1.605992 CCTGGCCTCTGCATCAGAA 59.394 57.895 3.32 0.00 40.18 3.02
674 3444 5.257082 TCAGAATGATGCATGAACATTGG 57.743 39.130 14.80 8.44 42.56 3.16
675 3445 4.707934 TCAGAATGATGCATGAACATTGGT 59.292 37.500 14.80 2.31 42.56 3.67
676 3446 5.041287 CAGAATGATGCATGAACATTGGTC 58.959 41.667 14.80 0.00 39.69 4.02
677 3447 3.703286 ATGATGCATGAACATTGGTCG 57.297 42.857 2.46 0.00 0.00 4.79
678 3448 2.709213 TGATGCATGAACATTGGTCGA 58.291 42.857 2.46 0.00 0.00 4.20
679 3449 2.419673 TGATGCATGAACATTGGTCGAC 59.580 45.455 2.46 7.13 0.00 4.20
763 3551 1.004979 ACTCTACTCCACGCCTTCTCT 59.995 52.381 0.00 0.00 0.00 3.10
804 3596 4.924462 CAGAGAACTCCGGAGAAAACTAAC 59.076 45.833 37.69 17.88 0.00 2.34
806 3598 4.884247 AGAACTCCGGAGAAAACTAACAG 58.116 43.478 37.69 7.99 0.00 3.16
807 3599 4.344390 AGAACTCCGGAGAAAACTAACAGT 59.656 41.667 37.69 8.72 0.00 3.55
808 3600 5.537674 AGAACTCCGGAGAAAACTAACAGTA 59.462 40.000 37.69 0.00 0.00 2.74
809 3601 5.997384 ACTCCGGAGAAAACTAACAGTAT 57.003 39.130 37.69 7.08 0.00 2.12
810 3602 6.356186 ACTCCGGAGAAAACTAACAGTATT 57.644 37.500 37.69 6.35 0.00 1.89
811 3603 6.766429 ACTCCGGAGAAAACTAACAGTATTT 58.234 36.000 37.69 5.92 0.00 1.40
812 3604 6.872547 ACTCCGGAGAAAACTAACAGTATTTC 59.127 38.462 37.69 0.00 31.52 2.17
813 3605 6.168389 TCCGGAGAAAACTAACAGTATTTCC 58.832 40.000 0.00 0.00 31.62 3.13
814 3606 5.935789 CCGGAGAAAACTAACAGTATTTCCA 59.064 40.000 0.00 0.00 31.62 3.53
816 3608 6.425721 CGGAGAAAACTAACAGTATTTCCACA 59.574 38.462 0.00 0.00 31.62 4.17
818 3610 7.227910 GGAGAAAACTAACAGTATTTCCACACA 59.772 37.037 0.00 0.00 31.62 3.72
819 3611 7.927048 AGAAAACTAACAGTATTTCCACACAC 58.073 34.615 0.00 0.00 31.62 3.82
822 3614 5.937111 ACTAACAGTATTTCCACACACCTT 58.063 37.500 0.00 0.00 0.00 3.50
824 3616 6.831868 ACTAACAGTATTTCCACACACCTTTT 59.168 34.615 0.00 0.00 0.00 2.27
825 3617 5.514274 ACAGTATTTCCACACACCTTTTG 57.486 39.130 0.00 0.00 0.00 2.44
826 3618 4.202111 ACAGTATTTCCACACACCTTTTGC 60.202 41.667 0.00 0.00 0.00 3.68
876 3690 2.482490 CGGGCCTATATATAACCGCACC 60.482 54.545 0.84 8.94 34.54 5.01
877 3691 2.482490 GGGCCTATATATAACCGCACCG 60.482 54.545 0.84 0.00 0.00 4.94
917 3731 3.626924 ACCACCGCACCTCACTCC 61.627 66.667 0.00 0.00 0.00 3.85
963 3802 0.322997 ACCTGCTAGCTCTCGAGTGT 60.323 55.000 17.23 3.81 0.00 3.55
964 3803 0.814457 CCTGCTAGCTCTCGAGTGTT 59.186 55.000 17.23 10.76 0.00 3.32
1116 3980 2.044946 GGCGGCTGGTCCTTCAAT 60.045 61.111 0.00 0.00 0.00 2.57
1419 5446 5.301835 ACTACTTCATATGCAGCATTCCT 57.698 39.130 14.58 0.00 0.00 3.36
1469 5496 4.838152 CACCGCCGCCTAGCATGT 62.838 66.667 0.00 0.00 0.00 3.21
1517 5565 3.395671 CACGACGAGCGAAACTTAATTG 58.604 45.455 0.00 0.00 44.57 2.32
1591 5653 9.791820 CTAGATCAATGTGCAATGTTTGATTTA 57.208 29.630 12.93 11.25 38.55 1.40
1740 5809 0.912486 AAAGGATGCGGCTAGGTCTT 59.088 50.000 0.00 0.00 0.00 3.01
1787 6135 8.788325 ATCTCAATCATGTGACATACCATATG 57.212 34.615 0.00 0.00 37.11 1.78
1864 6222 9.183368 TCTTATGAATATAGCATCGACTGAGAT 57.817 33.333 0.00 0.00 0.00 2.75
1865 6223 9.800433 CTTATGAATATAGCATCGACTGAGATT 57.200 33.333 0.00 0.00 0.00 2.40
1868 6226 8.972262 TGAATATAGCATCGACTGAGATTAAC 57.028 34.615 0.00 0.00 0.00 2.01
1869 6227 8.029522 TGAATATAGCATCGACTGAGATTAACC 58.970 37.037 0.00 0.00 0.00 2.85
1870 6228 5.791336 ATAGCATCGACTGAGATTAACCA 57.209 39.130 0.00 0.00 0.00 3.67
1878 6243 4.174762 GACTGAGATTAACCAAGTCGACC 58.825 47.826 13.01 0.00 0.00 4.79
1880 6245 2.094390 TGAGATTAACCAAGTCGACCGG 60.094 50.000 17.78 17.78 0.00 5.28
1934 6299 4.464951 ACTCAATTGATGCATGGTCAACAT 59.535 37.500 8.96 0.00 38.31 2.71
2027 6394 7.539712 AGGAGTGTCATTAAAACATATCACG 57.460 36.000 0.00 0.00 0.00 4.35
2044 6684 9.762933 ACATATCACGCATATGCATATATACAA 57.237 29.630 26.52 5.91 46.09 2.41
2141 6781 1.818674 TGCGAGATGAAGCTACTGTCA 59.181 47.619 0.00 0.00 0.00 3.58
2152 6795 6.970484 TGAAGCTACTGTCAAAGGAAATTTC 58.030 36.000 9.83 9.83 0.00 2.17
2174 6817 2.050168 GGTTGACCGTACGCGACA 60.050 61.111 15.93 7.25 41.33 4.35
2264 6908 7.548196 AAAACTACAAACTGATCGTCTGAAA 57.452 32.000 0.00 0.00 0.00 2.69
2265 6909 6.771188 AACTACAAACTGATCGTCTGAAAG 57.229 37.500 0.00 0.06 0.00 2.62
2269 6913 4.752101 ACAAACTGATCGTCTGAAAGGAAG 59.248 41.667 0.00 0.00 0.00 3.46
2275 6919 5.487433 TGATCGTCTGAAAGGAAGCATAAA 58.513 37.500 0.00 0.00 0.00 1.40
2282 6926 7.042725 CGTCTGAAAGGAAGCATAAAATCGATA 60.043 37.037 0.00 0.00 0.00 2.92
2319 6963 6.373186 TGTAGAGCTTATCTCGAATCGAAA 57.627 37.500 6.84 0.00 46.44 3.46
2323 6967 5.000012 AGCTTATCTCGAATCGAAACACT 58.000 39.130 6.84 0.00 34.74 3.55
2355 6999 5.663556 AGATTAGAAGGGACGAGGAAGAAAT 59.336 40.000 0.00 0.00 0.00 2.17
2356 7000 6.839657 AGATTAGAAGGGACGAGGAAGAAATA 59.160 38.462 0.00 0.00 0.00 1.40
2360 7004 4.739587 AGGGACGAGGAAGAAATAAGAC 57.260 45.455 0.00 0.00 0.00 3.01
2376 7020 8.056400 AGAAATAAGACTAGAGAGGAGCTTACA 58.944 37.037 0.00 0.00 0.00 2.41
2421 7072 1.683365 GGGCCCATCATGTGTGCTT 60.683 57.895 19.95 0.00 0.00 3.91
2428 7079 2.750712 CCATCATGTGTGCTTGATGTGA 59.249 45.455 16.69 0.00 46.88 3.58
2442 7093 3.165071 TGATGTGACTCAACTCAGCCTA 58.835 45.455 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.070445 GATGGATGGACCGGCAGAG 59.930 63.158 0.00 0.00 42.61 3.35
1 2 1.056125 ATGATGGATGGACCGGCAGA 61.056 55.000 0.00 0.00 42.61 4.26
2 3 0.686789 TATGATGGATGGACCGGCAG 59.313 55.000 0.00 0.00 42.61 4.85
5 6 3.676049 CGTGTATATGATGGATGGACCGG 60.676 52.174 0.00 0.00 42.61 5.28
7 8 4.495422 GACGTGTATATGATGGATGGACC 58.505 47.826 0.00 0.00 39.54 4.46
8 9 4.082949 TCGACGTGTATATGATGGATGGAC 60.083 45.833 0.00 0.00 0.00 4.02
9 10 4.076394 TCGACGTGTATATGATGGATGGA 58.924 43.478 0.00 0.00 0.00 3.41
10 11 4.415735 CTCGACGTGTATATGATGGATGG 58.584 47.826 0.00 0.00 0.00 3.51
11 12 3.854240 GCTCGACGTGTATATGATGGATG 59.146 47.826 0.00 0.00 0.00 3.51
12 13 3.426292 CGCTCGACGTGTATATGATGGAT 60.426 47.826 0.00 0.00 36.87 3.41
13 14 2.095919 CGCTCGACGTGTATATGATGGA 60.096 50.000 0.00 0.00 36.87 3.41
14 15 2.242564 CGCTCGACGTGTATATGATGG 58.757 52.381 0.00 0.00 36.87 3.51
15 16 2.242564 CCGCTCGACGTGTATATGATG 58.757 52.381 0.00 0.00 41.42 3.07
16 17 1.401148 GCCGCTCGACGTGTATATGAT 60.401 52.381 0.00 0.00 41.42 2.45
17 18 0.040692 GCCGCTCGACGTGTATATGA 60.041 55.000 0.00 0.00 41.42 2.15
18 19 1.002250 GGCCGCTCGACGTGTATATG 61.002 60.000 0.00 0.00 41.42 1.78
19 20 1.285023 GGCCGCTCGACGTGTATAT 59.715 57.895 0.00 0.00 41.42 0.86
20 21 2.055310 CTGGCCGCTCGACGTGTATA 62.055 60.000 0.00 0.00 41.42 1.47
21 22 3.411418 CTGGCCGCTCGACGTGTAT 62.411 63.158 0.00 0.00 41.42 2.29
22 23 4.111016 CTGGCCGCTCGACGTGTA 62.111 66.667 0.00 0.00 41.42 2.90
37 38 3.899981 TAACACTGGCTGGCCGCTG 62.900 63.158 17.07 11.21 39.42 5.18
38 39 2.484287 AATAACACTGGCTGGCCGCT 62.484 55.000 17.07 1.74 39.42 5.52
39 40 0.746563 TAATAACACTGGCTGGCCGC 60.747 55.000 10.60 10.60 39.42 6.53
40 41 1.967319 ATAATAACACTGGCTGGCCG 58.033 50.000 7.14 4.75 39.42 6.13
41 42 7.393234 TGATAATTATAATAACACTGGCTGGCC 59.607 37.037 4.43 4.43 0.00 5.36
42 43 8.237267 GTGATAATTATAATAACACTGGCTGGC 58.763 37.037 15.79 0.00 0.00 4.85
43 44 9.507329 AGTGATAATTATAATAACACTGGCTGG 57.493 33.333 20.79 0.00 36.11 4.85
87 88 9.901172 AAACTTATATTTAGGAACGAATGGAGT 57.099 29.630 0.00 0.00 0.00 3.85
119 120 8.353684 CCGTATGTAGTGTCTATTGAAATCTCT 58.646 37.037 0.00 0.00 0.00 3.10
120 121 8.350722 TCCGTATGTAGTGTCTATTGAAATCTC 58.649 37.037 0.00 0.00 0.00 2.75
121 122 8.234136 TCCGTATGTAGTGTCTATTGAAATCT 57.766 34.615 0.00 0.00 0.00 2.40
154 155 9.890629 TGTAAATCTGTGCTCTAAAATATGACT 57.109 29.630 0.00 0.00 0.00 3.41
155 156 9.922305 GTGTAAATCTGTGCTCTAAAATATGAC 57.078 33.333 0.00 0.00 0.00 3.06
156 157 9.665719 TGTGTAAATCTGTGCTCTAAAATATGA 57.334 29.630 0.00 0.00 0.00 2.15
161 162 9.462174 CAAAATGTGTAAATCTGTGCTCTAAAA 57.538 29.630 0.00 0.00 0.00 1.52
162 163 7.594758 GCAAAATGTGTAAATCTGTGCTCTAAA 59.405 33.333 0.00 0.00 0.00 1.85
163 164 7.040478 AGCAAAATGTGTAAATCTGTGCTCTAA 60.040 33.333 0.00 0.00 34.91 2.10
164 165 6.430925 AGCAAAATGTGTAAATCTGTGCTCTA 59.569 34.615 0.00 0.00 34.91 2.43
165 166 5.242393 AGCAAAATGTGTAAATCTGTGCTCT 59.758 36.000 0.00 0.00 34.91 4.09
166 167 5.464168 AGCAAAATGTGTAAATCTGTGCTC 58.536 37.500 0.00 0.00 34.91 4.26
167 168 5.458041 AGCAAAATGTGTAAATCTGTGCT 57.542 34.783 0.00 0.00 35.09 4.40
168 169 5.164158 CGAAGCAAAATGTGTAAATCTGTGC 60.164 40.000 0.00 0.00 0.00 4.57
169 170 5.914635 ACGAAGCAAAATGTGTAAATCTGTG 59.085 36.000 0.00 0.00 0.00 3.66
170 171 6.072112 ACGAAGCAAAATGTGTAAATCTGT 57.928 33.333 0.00 0.00 0.00 3.41
171 172 7.750458 ACATACGAAGCAAAATGTGTAAATCTG 59.250 33.333 0.00 0.00 31.56 2.90
172 173 7.816640 ACATACGAAGCAAAATGTGTAAATCT 58.183 30.769 0.00 0.00 31.56 2.40
173 174 9.210426 CTACATACGAAGCAAAATGTGTAAATC 57.790 33.333 0.00 0.00 34.54 2.17
174 175 8.726988 ACTACATACGAAGCAAAATGTGTAAAT 58.273 29.630 0.00 0.00 34.54 1.40
175 176 8.090250 ACTACATACGAAGCAAAATGTGTAAA 57.910 30.769 0.00 0.00 34.54 2.01
176 177 7.601130 AGACTACATACGAAGCAAAATGTGTAA 59.399 33.333 0.00 0.00 34.54 2.41
177 178 7.094631 AGACTACATACGAAGCAAAATGTGTA 58.905 34.615 0.00 0.00 34.54 2.90
178 179 5.932303 AGACTACATACGAAGCAAAATGTGT 59.068 36.000 0.00 0.00 34.54 3.72
179 180 6.408858 AGACTACATACGAAGCAAAATGTG 57.591 37.500 0.00 0.00 34.54 3.21
180 181 7.435068 AAAGACTACATACGAAGCAAAATGT 57.565 32.000 0.00 0.00 36.56 2.71
181 182 8.728088 AAAAAGACTACATACGAAGCAAAATG 57.272 30.769 0.00 0.00 0.00 2.32
230 231 9.225682 TGACTAATACTCCCTCCATTTCTAAAT 57.774 33.333 0.00 0.00 0.00 1.40
231 232 8.483758 GTGACTAATACTCCCTCCATTTCTAAA 58.516 37.037 0.00 0.00 0.00 1.85
232 233 7.844779 AGTGACTAATACTCCCTCCATTTCTAA 59.155 37.037 0.00 0.00 0.00 2.10
233 234 7.287927 CAGTGACTAATACTCCCTCCATTTCTA 59.712 40.741 0.00 0.00 0.00 2.10
234 235 6.098982 CAGTGACTAATACTCCCTCCATTTCT 59.901 42.308 0.00 0.00 0.00 2.52
235 236 6.284459 CAGTGACTAATACTCCCTCCATTTC 58.716 44.000 0.00 0.00 0.00 2.17
236 237 5.396884 GCAGTGACTAATACTCCCTCCATTT 60.397 44.000 0.00 0.00 0.00 2.32
237 238 4.101741 GCAGTGACTAATACTCCCTCCATT 59.898 45.833 0.00 0.00 0.00 3.16
238 239 3.643792 GCAGTGACTAATACTCCCTCCAT 59.356 47.826 0.00 0.00 0.00 3.41
239 240 3.031736 GCAGTGACTAATACTCCCTCCA 58.968 50.000 0.00 0.00 0.00 3.86
240 241 2.365941 GGCAGTGACTAATACTCCCTCC 59.634 54.545 0.00 0.00 0.00 4.30
241 242 2.365941 GGGCAGTGACTAATACTCCCTC 59.634 54.545 0.00 0.00 34.96 4.30
242 243 2.399580 GGGCAGTGACTAATACTCCCT 58.600 52.381 0.00 0.00 34.96 4.20
243 244 1.416772 GGGGCAGTGACTAATACTCCC 59.583 57.143 0.00 0.00 36.04 4.30
244 245 1.068741 CGGGGCAGTGACTAATACTCC 59.931 57.143 0.00 0.00 0.00 3.85
245 246 1.538419 GCGGGGCAGTGACTAATACTC 60.538 57.143 0.00 0.00 0.00 2.59
246 247 0.464452 GCGGGGCAGTGACTAATACT 59.536 55.000 0.00 0.00 0.00 2.12
247 248 0.177141 TGCGGGGCAGTGACTAATAC 59.823 55.000 0.00 0.00 33.32 1.89
248 249 0.906066 TTGCGGGGCAGTGACTAATA 59.094 50.000 0.00 0.00 40.61 0.98
249 250 0.676782 GTTGCGGGGCAGTGACTAAT 60.677 55.000 0.00 0.00 40.61 1.73
250 251 1.302192 GTTGCGGGGCAGTGACTAA 60.302 57.895 0.00 0.00 40.61 2.24
251 252 2.345991 GTTGCGGGGCAGTGACTA 59.654 61.111 0.00 0.00 40.61 2.59
252 253 4.988598 CGTTGCGGGGCAGTGACT 62.989 66.667 0.00 0.00 40.61 3.41
253 254 4.980805 TCGTTGCGGGGCAGTGAC 62.981 66.667 0.00 0.00 40.61 3.67
254 255 4.980805 GTCGTTGCGGGGCAGTGA 62.981 66.667 0.00 0.00 40.61 3.41
255 256 4.988598 AGTCGTTGCGGGGCAGTG 62.989 66.667 0.00 0.00 40.61 3.66
256 257 4.681978 GAGTCGTTGCGGGGCAGT 62.682 66.667 0.00 0.00 40.61 4.40
257 258 3.001902 TAGAGTCGTTGCGGGGCAG 62.002 63.158 0.00 0.00 40.61 4.85
258 259 2.992689 TAGAGTCGTTGCGGGGCA 60.993 61.111 0.00 0.00 36.47 5.36
259 260 2.508663 GTAGAGTCGTTGCGGGGC 60.509 66.667 0.00 0.00 0.00 5.80
260 261 1.647545 TACGTAGAGTCGTTGCGGGG 61.648 60.000 0.00 0.00 43.80 5.73
261 262 0.379669 ATACGTAGAGTCGTTGCGGG 59.620 55.000 0.08 0.00 43.80 6.13
262 263 1.063027 TCATACGTAGAGTCGTTGCGG 59.937 52.381 0.08 0.00 43.80 5.69
263 264 2.222976 ACTCATACGTAGAGTCGTTGCG 60.223 50.000 16.89 1.49 42.40 4.85
264 265 3.402058 ACTCATACGTAGAGTCGTTGC 57.598 47.619 16.89 0.00 42.40 4.17
265 266 5.907945 CCATAACTCATACGTAGAGTCGTTG 59.092 44.000 20.57 17.61 45.11 4.10
266 267 5.819379 TCCATAACTCATACGTAGAGTCGTT 59.181 40.000 20.57 15.14 45.11 3.85
287 288 5.063060 CGACGTGTATATGATACTCGATCCA 59.937 44.000 21.27 0.00 37.70 3.41
322 323 3.627577 GCATTGGAGTCGACATATTTGGT 59.372 43.478 19.50 0.00 0.00 3.67
352 368 7.330946 TCAACACCGTCAGATTAATCTTAACTG 59.669 37.037 15.49 14.17 34.22 3.16
353 369 7.383687 TCAACACCGTCAGATTAATCTTAACT 58.616 34.615 15.49 0.46 34.22 2.24
370 386 0.320771 CCAAGTCCCTCTCAACACCG 60.321 60.000 0.00 0.00 0.00 4.94
400 423 4.663140 CGCGCACCATACGTATAATCAAAG 60.663 45.833 7.96 0.00 0.00 2.77
401 424 3.182772 CGCGCACCATACGTATAATCAAA 59.817 43.478 7.96 0.00 0.00 2.69
402 425 2.727278 CGCGCACCATACGTATAATCAA 59.273 45.455 7.96 0.00 0.00 2.57
403 426 2.321263 CGCGCACCATACGTATAATCA 58.679 47.619 7.96 0.00 0.00 2.57
404 427 1.652124 CCGCGCACCATACGTATAATC 59.348 52.381 7.96 0.00 0.00 1.75
405 428 1.000060 ACCGCGCACCATACGTATAAT 60.000 47.619 7.96 0.00 0.00 1.28
406 429 0.385029 ACCGCGCACCATACGTATAA 59.615 50.000 7.96 0.00 0.00 0.98
435 458 3.365535 GCAAAGGTGGCGTCCAAT 58.634 55.556 0.00 0.00 34.18 3.16
496 524 5.108385 ACTTAGCGTGGAAACATTTGAAG 57.892 39.130 0.00 0.00 46.14 3.02
498 526 5.178623 CACTACTTAGCGTGGAAACATTTGA 59.821 40.000 0.00 0.00 46.14 2.69
499 527 5.382303 CACTACTTAGCGTGGAAACATTTG 58.618 41.667 0.00 0.00 46.14 2.32
500 528 5.607119 CACTACTTAGCGTGGAAACATTT 57.393 39.130 0.00 0.00 46.14 2.32
509 537 1.518572 CCGGCCACTACTTAGCGTG 60.519 63.158 2.24 0.00 0.00 5.34
592 3344 2.686956 TTCTGCTCGACGGCGACAAA 62.687 55.000 10.67 7.83 42.51 2.83
629 3385 2.367512 AGGCCAGGGGTGATCCTC 60.368 66.667 5.01 0.00 34.31 3.71
637 3393 3.414193 TGATGCAGAGGCCAGGGG 61.414 66.667 5.01 0.00 40.13 4.79
640 3396 1.134189 TCATTCTGATGCAGAGGCCAG 60.134 52.381 5.01 0.00 41.75 4.85
655 3411 4.039703 CGACCAATGTTCATGCATCATTC 58.960 43.478 8.68 0.00 30.74 2.67
656 3412 3.695556 TCGACCAATGTTCATGCATCATT 59.304 39.130 0.00 0.71 32.93 2.57
657 3413 3.065786 GTCGACCAATGTTCATGCATCAT 59.934 43.478 3.51 0.00 0.00 2.45
667 3437 0.107081 TTGGACCGTCGACCAATGTT 59.893 50.000 10.58 0.00 40.59 2.71
668 3438 0.107081 TTTGGACCGTCGACCAATGT 59.893 50.000 19.00 2.03 44.10 2.71
669 3439 0.796312 CTTTGGACCGTCGACCAATG 59.204 55.000 19.00 17.44 44.10 2.82
670 3440 0.395312 ACTTTGGACCGTCGACCAAT 59.605 50.000 19.00 7.64 44.10 3.16
671 3441 0.178533 AACTTTGGACCGTCGACCAA 59.821 50.000 10.58 15.98 43.22 3.67
672 3442 1.039068 TAACTTTGGACCGTCGACCA 58.961 50.000 10.58 0.00 0.00 4.02
673 3443 2.064014 CTTAACTTTGGACCGTCGACC 58.936 52.381 10.58 0.00 0.00 4.79
674 3444 1.458445 GCTTAACTTTGGACCGTCGAC 59.542 52.381 5.18 5.18 0.00 4.20
675 3445 1.068895 TGCTTAACTTTGGACCGTCGA 59.931 47.619 0.00 0.00 0.00 4.20
676 3446 1.504359 TGCTTAACTTTGGACCGTCG 58.496 50.000 0.00 0.00 0.00 5.12
677 3447 4.499037 AATTGCTTAACTTTGGACCGTC 57.501 40.909 0.00 0.00 0.00 4.79
678 3448 4.929819 AAATTGCTTAACTTTGGACCGT 57.070 36.364 0.00 0.00 0.00 4.83
679 3449 6.310224 CCATTAAATTGCTTAACTTTGGACCG 59.690 38.462 0.00 0.00 32.30 4.79
763 3551 6.101650 TCTCTGTTGCTGTATTCTTCTTCA 57.898 37.500 0.00 0.00 0.00 3.02
804 3596 4.298332 GCAAAAGGTGTGTGGAAATACTG 58.702 43.478 0.00 0.00 0.00 2.74
806 3598 3.554129 GGGCAAAAGGTGTGTGGAAATAC 60.554 47.826 0.00 0.00 0.00 1.89
807 3599 2.630580 GGGCAAAAGGTGTGTGGAAATA 59.369 45.455 0.00 0.00 0.00 1.40
808 3600 1.416030 GGGCAAAAGGTGTGTGGAAAT 59.584 47.619 0.00 0.00 0.00 2.17
809 3601 0.827368 GGGCAAAAGGTGTGTGGAAA 59.173 50.000 0.00 0.00 0.00 3.13
810 3602 0.032615 AGGGCAAAAGGTGTGTGGAA 60.033 50.000 0.00 0.00 0.00 3.53
811 3603 0.847373 TAGGGCAAAAGGTGTGTGGA 59.153 50.000 0.00 0.00 0.00 4.02
812 3604 0.958822 GTAGGGCAAAAGGTGTGTGG 59.041 55.000 0.00 0.00 0.00 4.17
813 3605 1.981256 AGTAGGGCAAAAGGTGTGTG 58.019 50.000 0.00 0.00 0.00 3.82
814 3606 2.306847 CAAGTAGGGCAAAAGGTGTGT 58.693 47.619 0.00 0.00 0.00 3.72
816 3608 1.328279 GCAAGTAGGGCAAAAGGTGT 58.672 50.000 0.00 0.00 0.00 4.16
818 3610 0.541998 GGGCAAGTAGGGCAAAAGGT 60.542 55.000 0.00 0.00 34.52 3.50
819 3611 0.251787 AGGGCAAGTAGGGCAAAAGG 60.252 55.000 0.00 0.00 34.52 3.11
822 3614 0.251165 GTGAGGGCAAGTAGGGCAAA 60.251 55.000 0.00 0.00 34.52 3.68
824 3616 2.954684 CGTGAGGGCAAGTAGGGCA 61.955 63.158 0.00 0.00 34.52 5.36
825 3617 2.125106 CGTGAGGGCAAGTAGGGC 60.125 66.667 0.00 0.00 0.00 5.19
826 3618 2.125106 GCGTGAGGGCAAGTAGGG 60.125 66.667 0.00 0.00 0.00 3.53
876 3690 2.588877 CAATGGACTAGCCGCCCG 60.589 66.667 0.00 0.00 40.66 6.13
877 3691 2.902343 GCAATGGACTAGCCGCCC 60.902 66.667 0.00 0.00 40.66 6.13
878 3692 2.902343 GGCAATGGACTAGCCGCC 60.902 66.667 0.00 0.00 38.86 6.13
917 3731 2.102252 GAGAAGCAGAGGAGGTATGTGG 59.898 54.545 0.00 0.00 0.00 4.17
963 3802 2.227865 GAGCGCCTACCAATCAAACAAA 59.772 45.455 2.29 0.00 0.00 2.83
964 3803 1.810151 GAGCGCCTACCAATCAAACAA 59.190 47.619 2.29 0.00 0.00 2.83
1466 5493 2.228241 CGCGCGTACGATGGAACAT 61.228 57.895 24.19 0.00 43.93 2.71
1495 5543 1.411394 TTAAGTTTCGCTCGTCGTGG 58.589 50.000 0.00 0.00 39.67 4.94
1517 5565 4.723248 CTCGGTCTTTTATTTTGGTCAGC 58.277 43.478 0.00 0.00 0.00 4.26
1534 5594 2.126580 GAAGCACGTACGCTCGGT 60.127 61.111 16.72 7.01 42.89 4.69
1740 5809 6.433404 AGATTTGGTTAACTCTCAGTCGACTA 59.567 38.462 19.57 1.41 0.00 2.59
1837 6195 9.183368 TCTCAGTCGATGCTATATTCATAAGAT 57.817 33.333 0.00 0.00 0.00 2.40
1864 6222 3.405823 AATTCCGGTCGACTTGGTTAA 57.594 42.857 21.39 13.00 0.00 2.01
1865 6223 3.405823 AAATTCCGGTCGACTTGGTTA 57.594 42.857 21.39 13.87 0.00 2.85
1866 6224 2.265589 AAATTCCGGTCGACTTGGTT 57.734 45.000 21.39 10.77 0.00 3.67
1868 6226 3.068560 TGTTAAATTCCGGTCGACTTGG 58.931 45.455 16.46 17.26 0.00 3.61
1869 6227 4.024725 TGTTGTTAAATTCCGGTCGACTTG 60.025 41.667 16.46 8.41 0.00 3.16
1870 6228 4.128643 TGTTGTTAAATTCCGGTCGACTT 58.871 39.130 16.46 3.00 0.00 3.01
1958 6323 9.606631 GACCCTCATTTCATCCAACTATATATC 57.393 37.037 0.00 0.00 0.00 1.63
1959 6324 8.552296 GGACCCTCATTTCATCCAACTATATAT 58.448 37.037 0.00 0.00 0.00 0.86
1960 6325 7.739444 AGGACCCTCATTTCATCCAACTATATA 59.261 37.037 0.00 0.00 31.41 0.86
1961 6326 6.564152 AGGACCCTCATTTCATCCAACTATAT 59.436 38.462 0.00 0.00 31.41 0.86
1988 6353 2.441001 CACTCCTTAGGGCATCTCCAAT 59.559 50.000 0.00 0.00 36.21 3.16
2044 6684 8.954834 AGTAGATCTACATCTTCCTCATGAAT 57.045 34.615 29.85 5.19 40.18 2.57
2141 6781 5.113383 GGTCAACCGTTTGAAATTTCCTTT 58.887 37.500 15.48 0.00 43.52 3.11
2167 6810 4.800993 TGAATTTTGTCAAATTTGTCGCGT 59.199 33.333 17.47 0.00 41.79 6.01
2201 6845 7.037438 GCTCAATTTTGTGTTCATGTATGGAT 58.963 34.615 0.00 0.00 0.00 3.41
2248 6892 3.748568 GCTTCCTTTCAGACGATCAGTTT 59.251 43.478 0.00 0.00 0.00 2.66
2294 6938 7.668525 TTCGATTCGAGATAAGCTCTACATA 57.331 36.000 8.98 0.00 41.66 2.29
2295 6939 6.561737 TTCGATTCGAGATAAGCTCTACAT 57.438 37.500 8.98 0.00 41.66 2.29
2323 6967 4.768448 TCGTCCCTTCTAATCTACACAACA 59.232 41.667 0.00 0.00 0.00 3.33
2355 6999 6.039941 GCAATGTAAGCTCCTCTCTAGTCTTA 59.960 42.308 0.00 0.00 0.00 2.10
2356 7000 5.163457 GCAATGTAAGCTCCTCTCTAGTCTT 60.163 44.000 0.00 0.00 0.00 3.01
2360 7004 4.099266 AGTGCAATGTAAGCTCCTCTCTAG 59.901 45.833 0.00 0.00 0.00 2.43
2390 7034 4.344865 GGCCCCCTTGCACGAGAA 62.345 66.667 0.00 0.00 0.00 2.87
2395 7045 3.684369 ATGATGGGCCCCCTTGCAC 62.684 63.158 22.27 3.14 36.94 4.57
2421 7072 1.973515 AGGCTGAGTTGAGTCACATCA 59.026 47.619 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.