Multiple sequence alignment - TraesCS5A01G077700

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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 TraesCS5A01G077700 chr5A 100.000 3834 0 0 1 3834 94747519 94743686 0.000000e+00 7081.0
1 TraesCS5A01G077700 chr5A 86.111 72 8 2 1574 1644 539960845 539960775 4.110000e-10 76.8
2 TraesCS5A01G077700 chr5D 94.811 3064 114 16 1 3052 103634242 103637272 0.000000e+00 4735.0
3 TraesCS5A01G077700 chr5D 94.810 289 13 1 3258 3546 103637907 103638193 2.100000e-122 449.0
4 TraesCS5A01G077700 chr5D 91.319 288 25 0 3547 3834 103644246 103644533 9.980000e-106 394.0
5 TraesCS5A01G077700 chr5D 95.431 197 9 0 3050 3246 103637597 103637793 8.000000e-82 315.0
6 TraesCS5A01G077700 chr5D 91.716 169 14 0 2431 2599 150835567 150835735 6.400000e-58 235.0
7 TraesCS5A01G077700 chr5D 85.714 196 19 5 473 661 437985001 437985194 8.400000e-47 198.0
8 TraesCS5A01G077700 chr5D 79.386 228 32 10 458 672 425895816 425896041 3.090000e-31 147.0
9 TraesCS5A01G077700 chr5D 85.294 136 18 2 330 465 211916310 211916177 5.160000e-29 139.0
10 TraesCS5A01G077700 chr5D 85.714 133 17 2 330 462 425892969 425893099 5.160000e-29 139.0
11 TraesCS5A01G077700 chr5D 83.784 74 7 5 1574 1644 425721496 425721425 8.890000e-07 65.8
12 TraesCS5A01G077700 chr4B 91.634 1781 111 19 41 1795 575780823 575779055 0.000000e+00 2429.0
13 TraesCS5A01G077700 chr4B 91.882 271 20 2 2630 2899 575778025 575777756 1.010000e-100 377.0
14 TraesCS5A01G077700 chr4B 86.782 348 32 4 1987 2320 575778667 575778320 3.620000e-100 375.0
15 TraesCS5A01G077700 chr4B 92.308 195 13 2 1796 1989 575778942 575778749 3.770000e-70 276.0
16 TraesCS5A01G077700 chr4B 90.698 172 14 2 2428 2599 549841919 549841750 1.070000e-55 228.0
17 TraesCS5A01G077700 chr5B 93.741 1422 76 8 1 1413 112573496 112574913 0.000000e+00 2121.0
18 TraesCS5A01G077700 chr5B 94.486 399 21 1 1469 1867 112574914 112575311 7.040000e-172 614.0
19 TraesCS5A01G077700 chr5B 93.878 245 14 1 3590 3834 112585450 112585693 6.050000e-98 368.0
20 TraesCS5A01G077700 chr5B 92.121 165 13 0 2432 2596 316709146 316708982 2.300000e-57 233.0
21 TraesCS5A01G077700 chr5B 86.029 136 17 2 330 465 81578397 81578264 1.110000e-30 145.0
22 TraesCS5A01G077700 chr5B 84.892 139 19 2 330 468 532564863 532564727 5.160000e-29 139.0
23 TraesCS5A01G077700 chr4A 86.937 222 21 7 458 672 174618796 174618576 3.830000e-60 243.0
24 TraesCS5A01G077700 chr4D 92.727 165 12 0 2432 2596 386984668 386984832 4.950000e-59 239.0
25 TraesCS5A01G077700 chr4D 89.773 176 16 2 2431 2606 465125472 465125299 1.390000e-54 224.0
26 TraesCS5A01G077700 chr3D 92.593 162 12 0 2432 2593 87926000 87926161 2.300000e-57 233.0
27 TraesCS5A01G077700 chr2B 90.503 179 12 2 2423 2596 212577430 212577252 8.280000e-57 231.0
28 TraesCS5A01G077700 chr1D 91.176 170 15 0 2429 2598 103408715 103408884 8.280000e-57 231.0
29 TraesCS5A01G077700 chr6B 85.068 221 27 3 458 672 494281874 494282094 1.790000e-53 220.0
30 TraesCS5A01G077700 chr7D 84.259 216 27 4 458 668 167405623 167405410 1.810000e-48 204.0
31 TraesCS5A01G077700 chr3B 82.759 232 22 11 458 672 815222065 815221835 1.410000e-44 191.0
32 TraesCS5A01G077700 chr3B 85.294 136 18 2 330 465 727940177 727940044 5.160000e-29 139.0
33 TraesCS5A01G077700 chr3B 85.000 140 16 2 327 462 43922231 43922369 1.860000e-28 137.0
34 TraesCS5A01G077700 chr3B 89.189 74 8 0 1585 1658 782841689 782841616 4.080000e-15 93.5
35 TraesCS5A01G077700 chr1A 91.667 72 4 2 1585 1655 36563561 36563491 8.770000e-17 99.0
36 TraesCS5A01G077700 chr1A 93.443 61 2 2 1585 1644 234813505 234813564 5.280000e-14 89.8
37 TraesCS5A01G077700 chr1B 94.737 57 3 0 1585 1641 223137635 223137579 5.280000e-14 89.8


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 TraesCS5A01G077700 chr5A 94743686 94747519 3833 True 7081.00 7081 100.000000 1 3834 1 chr5A.!!$R1 3833
1 TraesCS5A01G077700 chr5D 103634242 103638193 3951 False 1833.00 4735 95.017333 1 3546 3 chr5D.!!$F4 3545
2 TraesCS5A01G077700 chr4B 575777756 575780823 3067 True 864.25 2429 90.651500 41 2899 4 chr4B.!!$R2 2858
3 TraesCS5A01G077700 chr5B 112573496 112575311 1815 False 1367.50 2121 94.113500 1 1867 2 chr5B.!!$F2 1866

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
833 868 2.360350 CTCCGCTGCCAACCACAT 60.360 61.111 0.00 0.0 0.00 3.21 F
1350 1386 0.034186 ATTTGATCAAGGAGCGGCCA 60.034 50.000 8.41 0.0 40.02 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2767 3184 0.323178 CCAACTCTGCATCAAGGCCT 60.323 55.0 0.0 0.0 0.0 5.19 R
2996 3413 0.257039 CCATCACAAAGGGGGAGGAG 59.743 60.0 0.0 0.0 0.0 3.69 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
39 40 2.915659 AGCAGTCCGTCCGTCCAA 60.916 61.111 0.00 0.00 0.00 3.53
149 152 9.833894 CTTTGTGTTTAATTGAAACTTGAATCG 57.166 29.630 0.00 0.00 46.53 3.34
205 208 3.551846 GAACCAACCAAGACTCCAAGAA 58.448 45.455 0.00 0.00 0.00 2.52
299 303 6.166279 TGAACCAACTATTCAGTCATCTCAC 58.834 40.000 0.00 0.00 32.29 3.51
619 640 9.617523 GGGTAGTTATAAGTGCCAAAGTTATTA 57.382 33.333 23.84 0.00 36.14 0.98
662 685 3.092301 AGGCTTTGCTTTAATCCTGGAC 58.908 45.455 0.00 0.00 0.00 4.02
833 868 2.360350 CTCCGCTGCCAACCACAT 60.360 61.111 0.00 0.00 0.00 3.21
1350 1386 0.034186 ATTTGATCAAGGAGCGGCCA 60.034 50.000 8.41 0.00 40.02 5.36
1499 1536 1.131638 TGTCTGGAGACCTTGTTGCT 58.868 50.000 4.34 0.00 44.15 3.91
1576 1613 9.737427 CCTATGTAATAACTAGTGTGAGTCAAG 57.263 37.037 0.00 0.00 0.00 3.02
2008 2243 1.652563 GAGCCAAACCGTTGACACC 59.347 57.895 0.00 0.00 36.83 4.16
2096 2344 4.603131 TGGTAATACGTAGGAAGTGACCT 58.397 43.478 0.08 0.00 43.32 3.85
2101 2349 6.847421 AATACGTAGGAAGTGACCTAAGTT 57.153 37.500 15.59 4.94 46.97 2.66
2105 2353 5.245526 ACGTAGGAAGTGACCTAAGTTCAAT 59.754 40.000 0.00 0.00 46.97 2.57
2110 2358 2.301870 AGTGACCTAAGTTCAATCGGCA 59.698 45.455 0.00 0.00 0.00 5.69
2186 2439 5.640357 TCATTACGAAAACACTATGGTGGTC 59.360 40.000 14.25 6.91 43.38 4.02
2232 2485 3.242543 CGCTGATTCAACTACTTCATGGC 60.243 47.826 0.00 0.00 0.00 4.40
2356 2773 2.415697 AACCTTTTTCAACGATGGCG 57.584 45.000 0.00 0.00 44.79 5.69
2415 2832 1.183676 AGGTTACTTCGACCACCGCT 61.184 55.000 0.00 0.00 39.71 5.52
2506 2923 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
2538 2955 9.719355 TCTAAAATACGTCTATATACACCCGTA 57.281 33.333 0.00 0.00 35.57 4.02
2568 2985 9.753674 AGTTCATATTGAAATCTGTAAAAGGGA 57.246 29.630 0.00 0.00 38.22 4.20
2598 3015 7.451731 TTTAGAAATGGAGGGAGTACATCAT 57.548 36.000 0.00 0.00 0.00 2.45
2599 3016 5.559148 AGAAATGGAGGGAGTACATCATC 57.441 43.478 0.00 0.00 0.00 2.92
2600 3017 4.971282 AGAAATGGAGGGAGTACATCATCA 59.029 41.667 0.00 0.00 0.00 3.07
2653 3070 8.728088 AGTTATTTTTCTTATTGAACAGTGCG 57.272 30.769 0.00 0.00 33.88 5.34
2677 3094 0.896923 TTGTCGGTGTAATAGCCCGT 59.103 50.000 0.00 0.00 42.30 5.28
2686 3103 5.984926 CGGTGTAATAGCCCGTTTAATTAGA 59.015 40.000 0.00 0.00 37.00 2.10
2695 3112 4.095334 GCCCGTTTAATTAGATTCACGGTT 59.905 41.667 16.70 0.00 42.94 4.44
2767 3184 1.745890 CGACTGGGAGTTGTGTGGA 59.254 57.895 0.00 0.00 0.00 4.02
2839 3256 4.223659 CACTGCACGGTGGTTAATTTTAC 58.776 43.478 10.60 0.00 33.95 2.01
2852 3269 8.663025 GTGGTTAATTTTACTTCTACTGTAGGC 58.337 37.037 14.47 0.00 0.00 3.93
2862 3279 2.174210 TCTACTGTAGGCTACCGATGGT 59.826 50.000 21.34 13.67 40.16 3.55
2909 3326 9.762933 AACTAAATGCACTGTAATTTTCAATGT 57.237 25.926 0.00 0.00 0.00 2.71
2910 3327 9.410556 ACTAAATGCACTGTAATTTTCAATGTC 57.589 29.630 0.00 0.00 0.00 3.06
2996 3413 7.897864 ACTCATTACTACTATAACCAGGATGC 58.102 38.462 0.00 0.00 31.97 3.91
3002 3419 3.243724 ACTATAACCAGGATGCTCCTCC 58.756 50.000 0.00 0.00 45.66 4.30
3028 3445 5.413309 TTTGTGATGGTTTTGGAACAGTT 57.587 34.783 0.00 0.00 42.39 3.16
3082 3826 4.700213 AGTGGGAAAACTATTTGGACGATG 59.300 41.667 0.00 0.00 0.00 3.84
3083 3827 4.698304 GTGGGAAAACTATTTGGACGATGA 59.302 41.667 0.00 0.00 0.00 2.92
3132 3876 2.706890 ACTGGCGGTACTGTAAAATGG 58.293 47.619 0.00 0.00 0.00 3.16
3176 3920 2.726989 CGCAATAGCAAGTTCAGTGCAG 60.727 50.000 0.00 0.00 44.74 4.41
3191 3935 4.988540 TCAGTGCAGTAGTGTGTTTGATAC 59.011 41.667 0.00 0.00 0.00 2.24
3231 3975 6.824305 AGGATTCAAGTCGAAATCAATGTT 57.176 33.333 9.21 0.00 37.12 2.71
3234 3978 7.040478 AGGATTCAAGTCGAAATCAATGTTTGA 60.040 33.333 9.21 0.00 38.69 2.69
3298 4144 3.462427 TGCCATTGCATTGCATTCC 57.538 47.368 12.95 3.39 44.23 3.01
3299 4145 0.613777 TGCCATTGCATTGCATTCCA 59.386 45.000 12.95 5.85 44.23 3.53
3335 4181 4.572985 TCTTGAGCAAAGTTTGGTGATG 57.427 40.909 24.13 17.35 42.23 3.07
3337 4183 5.129634 TCTTGAGCAAAGTTTGGTGATGTA 58.870 37.500 24.13 1.23 42.23 2.29
3374 4220 5.993055 TGAAATTCAGATGAGTGATGCCTA 58.007 37.500 0.00 0.00 0.00 3.93
3375 4221 6.598503 TGAAATTCAGATGAGTGATGCCTAT 58.401 36.000 0.00 0.00 0.00 2.57
3391 4237 8.093307 GTGATGCCTATTAATTCAGAGATGAGA 58.907 37.037 0.00 0.00 0.00 3.27
3401 4247 3.639952 TCAGAGATGAGATTCAGAGCCA 58.360 45.455 0.00 0.00 0.00 4.75
3405 4251 3.047115 AGATGAGATTCAGAGCCATGGT 58.953 45.455 14.67 0.00 0.00 3.55
3406 4252 2.996249 TGAGATTCAGAGCCATGGTC 57.004 50.000 14.67 9.77 0.00 4.02
3446 4292 7.581476 TGTTTCTCAGTTAAATTGGACGATTC 58.419 34.615 0.00 0.00 0.00 2.52
3477 4323 4.081406 TGCAGAAGTATGCTTTCCATGTT 58.919 39.130 0.00 0.00 46.63 2.71
3553 4399 8.992349 TCTGGATGTATCCTTTCATAGAGAAAA 58.008 33.333 11.89 0.00 45.11 2.29
3554 4400 9.618890 CTGGATGTATCCTTTCATAGAGAAAAA 57.381 33.333 11.89 0.00 45.11 1.94
3555 4401 9.618890 TGGATGTATCCTTTCATAGAGAAAAAG 57.381 33.333 11.89 0.00 45.11 2.27
3556 4402 9.838339 GGATGTATCCTTTCATAGAGAAAAAGA 57.162 33.333 3.63 0.00 45.11 2.52
3559 4405 9.877178 TGTATCCTTTCATAGAGAAAAAGACTC 57.123 33.333 0.00 0.00 45.11 3.36
3560 4406 9.026074 GTATCCTTTCATAGAGAAAAAGACTCG 57.974 37.037 0.00 0.00 45.11 4.18
3561 4407 5.869888 TCCTTTCATAGAGAAAAAGACTCGC 59.130 40.000 0.00 0.00 45.11 5.03
3562 4408 5.872070 CCTTTCATAGAGAAAAAGACTCGCT 59.128 40.000 0.00 0.00 45.11 4.93
3563 4409 7.036220 CCTTTCATAGAGAAAAAGACTCGCTA 58.964 38.462 0.00 0.00 45.11 4.26
3564 4410 7.221838 CCTTTCATAGAGAAAAAGACTCGCTAG 59.778 40.741 0.00 0.00 45.11 3.42
3565 4411 6.761099 TCATAGAGAAAAAGACTCGCTAGT 57.239 37.500 0.00 0.00 39.12 2.57
3566 4412 7.159322 TCATAGAGAAAAAGACTCGCTAGTT 57.841 36.000 0.00 0.00 39.12 2.24
3567 4413 7.251994 TCATAGAGAAAAAGACTCGCTAGTTC 58.748 38.462 0.00 0.00 39.12 3.01
3568 4414 4.811908 AGAGAAAAAGACTCGCTAGTTCC 58.188 43.478 0.00 0.00 39.12 3.62
3569 4415 3.927758 GAGAAAAAGACTCGCTAGTTCCC 59.072 47.826 0.00 0.00 35.56 3.97
3570 4416 3.579151 AGAAAAAGACTCGCTAGTTCCCT 59.421 43.478 0.00 0.00 35.56 4.20
3571 4417 3.596310 AAAAGACTCGCTAGTTCCCTC 57.404 47.619 0.00 0.00 35.56 4.30
3572 4418 2.517998 AAGACTCGCTAGTTCCCTCT 57.482 50.000 0.00 0.00 35.56 3.69
3573 4419 1.757682 AGACTCGCTAGTTCCCTCTG 58.242 55.000 0.00 0.00 35.56 3.35
3574 4420 1.004979 AGACTCGCTAGTTCCCTCTGT 59.995 52.381 0.00 0.00 35.56 3.41
3575 4421 1.402613 GACTCGCTAGTTCCCTCTGTC 59.597 57.143 0.00 0.00 35.56 3.51
3576 4422 0.741915 CTCGCTAGTTCCCTCTGTCC 59.258 60.000 0.00 0.00 0.00 4.02
3577 4423 0.039180 TCGCTAGTTCCCTCTGTCCA 59.961 55.000 0.00 0.00 0.00 4.02
3578 4424 0.895530 CGCTAGTTCCCTCTGTCCAA 59.104 55.000 0.00 0.00 0.00 3.53
3579 4425 1.404315 CGCTAGTTCCCTCTGTCCAAC 60.404 57.143 0.00 0.00 0.00 3.77
3580 4426 1.623811 GCTAGTTCCCTCTGTCCAACA 59.376 52.381 0.00 0.00 0.00 3.33
3582 4428 1.807814 AGTTCCCTCTGTCCAACAGT 58.192 50.000 6.96 0.00 46.03 3.55
3583 4429 2.972348 AGTTCCCTCTGTCCAACAGTA 58.028 47.619 6.96 0.00 46.03 2.74
3584 4430 3.521727 AGTTCCCTCTGTCCAACAGTAT 58.478 45.455 6.96 0.00 46.03 2.12
3585 4431 3.261897 AGTTCCCTCTGTCCAACAGTATG 59.738 47.826 6.96 0.34 46.03 2.39
3602 4448 5.657474 CAGTATGTGTAAACCTATGTCGGT 58.343 41.667 0.00 0.00 39.48 4.69
3604 4450 6.035650 CAGTATGTGTAAACCTATGTCGGTTG 59.964 42.308 0.00 0.00 46.21 3.77
3605 4451 4.339872 TGTGTAAACCTATGTCGGTTGT 57.660 40.909 0.00 0.00 46.21 3.32
3606 4452 4.059511 TGTGTAAACCTATGTCGGTTGTG 58.940 43.478 0.00 0.00 46.21 3.33
3607 4453 4.060205 GTGTAAACCTATGTCGGTTGTGT 58.940 43.478 0.00 0.00 46.21 3.72
3608 4454 4.059511 TGTAAACCTATGTCGGTTGTGTG 58.940 43.478 0.00 0.00 46.21 3.82
3609 4455 3.478857 AAACCTATGTCGGTTGTGTGA 57.521 42.857 0.00 0.00 46.21 3.58
3610 4456 3.695830 AACCTATGTCGGTTGTGTGAT 57.304 42.857 0.00 0.00 45.24 3.06
3611 4457 4.811969 AACCTATGTCGGTTGTGTGATA 57.188 40.909 0.00 0.00 45.24 2.15
3612 4458 4.119442 ACCTATGTCGGTTGTGTGATAC 57.881 45.455 0.00 0.00 31.94 2.24
3613 4459 3.512329 ACCTATGTCGGTTGTGTGATACA 59.488 43.478 0.00 0.00 37.56 2.29
3614 4460 4.020928 ACCTATGTCGGTTGTGTGATACAA 60.021 41.667 0.00 0.00 46.62 2.41
3637 4483 9.450807 ACAAATAAATATGATCTGTTTAAGCGC 57.549 29.630 0.00 0.00 0.00 5.92
3638 4484 9.669353 CAAATAAATATGATCTGTTTAAGCGCT 57.331 29.630 2.64 2.64 0.00 5.92
3640 4486 9.669353 AATAAATATGATCTGTTTAAGCGCTTG 57.331 29.630 32.23 15.32 0.00 4.01
3641 4487 6.683974 AATATGATCTGTTTAAGCGCTTGT 57.316 33.333 32.23 10.24 0.00 3.16
3642 4488 4.606457 ATGATCTGTTTAAGCGCTTGTC 57.394 40.909 32.23 20.57 0.00 3.18
3643 4489 3.398406 TGATCTGTTTAAGCGCTTGTCA 58.602 40.909 32.23 23.55 0.00 3.58
3644 4490 3.812609 TGATCTGTTTAAGCGCTTGTCAA 59.187 39.130 32.23 16.23 0.00 3.18
3645 4491 4.455533 TGATCTGTTTAAGCGCTTGTCAAT 59.544 37.500 32.23 16.81 0.00 2.57
3646 4492 4.829064 TCTGTTTAAGCGCTTGTCAATT 57.171 36.364 32.23 6.85 0.00 2.32
3647 4493 4.536065 TCTGTTTAAGCGCTTGTCAATTG 58.464 39.130 32.23 15.26 0.00 2.32
3648 4494 4.036262 TCTGTTTAAGCGCTTGTCAATTGT 59.964 37.500 32.23 5.18 0.00 2.71
3649 4495 5.237561 TCTGTTTAAGCGCTTGTCAATTGTA 59.762 36.000 32.23 6.10 0.00 2.41
3650 4496 6.007936 TGTTTAAGCGCTTGTCAATTGTAT 57.992 33.333 32.23 3.76 0.00 2.29
3651 4497 6.083630 TGTTTAAGCGCTTGTCAATTGTATC 58.916 36.000 32.23 9.56 0.00 2.24
3652 4498 3.389687 AAGCGCTTGTCAATTGTATCG 57.610 42.857 24.40 4.93 0.00 2.92
3653 4499 2.616960 AGCGCTTGTCAATTGTATCGA 58.383 42.857 2.64 0.00 0.00 3.59
3654 4500 3.198068 AGCGCTTGTCAATTGTATCGAT 58.802 40.909 2.64 2.16 0.00 3.59
3655 4501 3.623060 AGCGCTTGTCAATTGTATCGATT 59.377 39.130 2.64 0.00 0.00 3.34
3656 4502 3.962481 GCGCTTGTCAATTGTATCGATTC 59.038 43.478 1.71 0.00 0.00 2.52
3657 4503 4.518217 CGCTTGTCAATTGTATCGATTCC 58.482 43.478 1.71 0.00 0.00 3.01
3658 4504 4.518217 GCTTGTCAATTGTATCGATTCCG 58.482 43.478 1.71 0.00 37.07 4.30
3659 4505 4.034048 GCTTGTCAATTGTATCGATTCCGT 59.966 41.667 1.71 0.00 37.05 4.69
3660 4506 5.233476 GCTTGTCAATTGTATCGATTCCGTA 59.767 40.000 1.71 0.00 37.05 4.02
3661 4507 6.073765 GCTTGTCAATTGTATCGATTCCGTAT 60.074 38.462 1.71 0.00 37.05 3.06
3662 4508 7.402811 TTGTCAATTGTATCGATTCCGTATC 57.597 36.000 1.71 0.00 37.05 2.24
3663 4509 6.508777 TGTCAATTGTATCGATTCCGTATCA 58.491 36.000 1.71 0.00 37.05 2.15
3664 4510 6.640907 TGTCAATTGTATCGATTCCGTATCAG 59.359 38.462 1.71 0.00 37.05 2.90
3665 4511 6.861572 GTCAATTGTATCGATTCCGTATCAGA 59.138 38.462 1.71 0.00 37.05 3.27
3666 4512 7.542477 GTCAATTGTATCGATTCCGTATCAGAT 59.458 37.037 1.71 0.00 37.05 2.90
3667 4513 8.736244 TCAATTGTATCGATTCCGTATCAGATA 58.264 33.333 1.71 0.00 37.05 1.98
3668 4514 9.353999 CAATTGTATCGATTCCGTATCAGATAA 57.646 33.333 1.71 0.00 34.09 1.75
3670 4516 9.737427 ATTGTATCGATTCCGTATCAGATAATC 57.263 33.333 1.71 0.00 34.09 1.75
3671 4517 7.704271 TGTATCGATTCCGTATCAGATAATCC 58.296 38.462 1.71 0.00 34.09 3.01
3672 4518 6.775594 ATCGATTCCGTATCAGATAATCCA 57.224 37.500 0.00 0.00 37.05 3.41
3673 4519 5.950883 TCGATTCCGTATCAGATAATCCAC 58.049 41.667 0.00 0.00 37.05 4.02
3674 4520 5.475564 TCGATTCCGTATCAGATAATCCACA 59.524 40.000 0.00 0.00 37.05 4.17
3675 4521 6.152831 TCGATTCCGTATCAGATAATCCACAT 59.847 38.462 0.00 0.00 37.05 3.21
3676 4522 7.338449 TCGATTCCGTATCAGATAATCCACATA 59.662 37.037 0.00 0.00 37.05 2.29
3677 4523 8.138074 CGATTCCGTATCAGATAATCCACATAT 58.862 37.037 0.00 0.00 32.45 1.78
3694 4540 9.835389 ATCCACATATAATTGGGAAAATTGTTG 57.165 29.630 3.71 0.00 33.25 3.33
3695 4541 9.040259 TCCACATATAATTGGGAAAATTGTTGA 57.960 29.630 3.71 0.00 33.25 3.18
3696 4542 9.835389 CCACATATAATTGGGAAAATTGTTGAT 57.165 29.630 0.00 0.00 0.00 2.57
3705 4551 8.572855 TTGGGAAAATTGTTGATTTTGAAAGT 57.427 26.923 1.82 0.00 45.54 2.66
3706 4552 8.572855 TGGGAAAATTGTTGATTTTGAAAGTT 57.427 26.923 1.82 0.00 45.54 2.66
3707 4553 8.457261 TGGGAAAATTGTTGATTTTGAAAGTTG 58.543 29.630 1.82 0.00 45.54 3.16
3708 4554 8.458052 GGGAAAATTGTTGATTTTGAAAGTTGT 58.542 29.630 1.82 0.00 45.54 3.32
3709 4555 9.276397 GGAAAATTGTTGATTTTGAAAGTTGTG 57.724 29.630 1.82 0.00 45.54 3.33
3710 4556 9.824534 GAAAATTGTTGATTTTGAAAGTTGTGT 57.175 25.926 1.82 0.00 45.54 3.72
3713 4559 8.647143 ATTGTTGATTTTGAAAGTTGTGTAGG 57.353 30.769 0.00 0.00 0.00 3.18
3714 4560 7.164230 TGTTGATTTTGAAAGTTGTGTAGGT 57.836 32.000 0.00 0.00 0.00 3.08
3715 4561 7.032580 TGTTGATTTTGAAAGTTGTGTAGGTG 58.967 34.615 0.00 0.00 0.00 4.00
3716 4562 6.767524 TGATTTTGAAAGTTGTGTAGGTGT 57.232 33.333 0.00 0.00 0.00 4.16
3717 4563 7.164230 TGATTTTGAAAGTTGTGTAGGTGTT 57.836 32.000 0.00 0.00 0.00 3.32
3718 4564 7.032580 TGATTTTGAAAGTTGTGTAGGTGTTG 58.967 34.615 0.00 0.00 0.00 3.33
3719 4565 5.968528 TTTGAAAGTTGTGTAGGTGTTGT 57.031 34.783 0.00 0.00 0.00 3.32
3720 4566 7.450124 TTTTGAAAGTTGTGTAGGTGTTGTA 57.550 32.000 0.00 0.00 0.00 2.41
3721 4567 7.633193 TTTGAAAGTTGTGTAGGTGTTGTAT 57.367 32.000 0.00 0.00 0.00 2.29
3722 4568 7.633193 TTGAAAGTTGTGTAGGTGTTGTATT 57.367 32.000 0.00 0.00 0.00 1.89
3723 4569 7.633193 TGAAAGTTGTGTAGGTGTTGTATTT 57.367 32.000 0.00 0.00 0.00 1.40
3724 4570 7.699566 TGAAAGTTGTGTAGGTGTTGTATTTC 58.300 34.615 0.00 0.00 0.00 2.17
3725 4571 7.554835 TGAAAGTTGTGTAGGTGTTGTATTTCT 59.445 33.333 0.00 0.00 0.00 2.52
3726 4572 6.861065 AGTTGTGTAGGTGTTGTATTTCTG 57.139 37.500 0.00 0.00 0.00 3.02
3727 4573 5.763204 AGTTGTGTAGGTGTTGTATTTCTGG 59.237 40.000 0.00 0.00 0.00 3.86
3728 4574 5.298989 TGTGTAGGTGTTGTATTTCTGGT 57.701 39.130 0.00 0.00 0.00 4.00
3729 4575 5.302360 TGTGTAGGTGTTGTATTTCTGGTC 58.698 41.667 0.00 0.00 0.00 4.02
3730 4576 4.387862 GTGTAGGTGTTGTATTTCTGGTCG 59.612 45.833 0.00 0.00 0.00 4.79
3731 4577 4.281435 TGTAGGTGTTGTATTTCTGGTCGA 59.719 41.667 0.00 0.00 0.00 4.20
3732 4578 4.345859 AGGTGTTGTATTTCTGGTCGAA 57.654 40.909 0.00 0.00 0.00 3.71
3733 4579 4.710324 AGGTGTTGTATTTCTGGTCGAAA 58.290 39.130 0.00 0.00 45.08 3.46
3734 4580 4.755123 AGGTGTTGTATTTCTGGTCGAAAG 59.245 41.667 0.00 0.00 44.29 2.62
3735 4581 4.083484 GGTGTTGTATTTCTGGTCGAAAGG 60.083 45.833 0.00 0.00 44.29 3.11
3736 4582 4.753107 GTGTTGTATTTCTGGTCGAAAGGA 59.247 41.667 0.00 0.00 44.29 3.36
3737 4583 4.994852 TGTTGTATTTCTGGTCGAAAGGAG 59.005 41.667 0.00 0.00 44.29 3.69
3738 4584 4.884668 TGTATTTCTGGTCGAAAGGAGT 57.115 40.909 0.00 0.00 44.29 3.85
3739 4585 5.988310 TGTATTTCTGGTCGAAAGGAGTA 57.012 39.130 0.00 0.00 44.29 2.59
3740 4586 5.717119 TGTATTTCTGGTCGAAAGGAGTAC 58.283 41.667 0.00 0.00 44.29 2.73
3741 4587 3.293311 TTTCTGGTCGAAAGGAGTACG 57.707 47.619 0.00 0.00 36.72 3.67
3742 4588 1.171308 TCTGGTCGAAAGGAGTACGG 58.829 55.000 0.00 0.00 0.00 4.02
3743 4589 0.458025 CTGGTCGAAAGGAGTACGGC 60.458 60.000 0.00 0.00 0.00 5.68
3744 4590 1.180456 TGGTCGAAAGGAGTACGGCA 61.180 55.000 0.00 0.00 33.22 5.69
3745 4591 0.735287 GGTCGAAAGGAGTACGGCAC 60.735 60.000 0.00 0.00 33.22 5.01
3746 4592 0.243095 GTCGAAAGGAGTACGGCACT 59.757 55.000 0.00 0.00 41.47 4.40
3781 4627 7.783090 TCGTCTCGAAATACTAGTATGAAGT 57.217 36.000 16.11 2.65 31.06 3.01
3782 4628 7.628235 TCGTCTCGAAATACTAGTATGAAGTG 58.372 38.462 16.11 10.57 31.06 3.16
3783 4629 6.851837 CGTCTCGAAATACTAGTATGAAGTGG 59.148 42.308 16.11 6.05 0.00 4.00
3784 4630 7.466996 CGTCTCGAAATACTAGTATGAAGTGGT 60.467 40.741 16.11 0.00 0.00 4.16
3785 4631 7.856894 GTCTCGAAATACTAGTATGAAGTGGTC 59.143 40.741 16.11 5.07 0.00 4.02
3786 4632 7.555195 TCTCGAAATACTAGTATGAAGTGGTCA 59.445 37.037 16.11 0.00 41.67 4.02
3787 4633 8.058667 TCGAAATACTAGTATGAAGTGGTCAA 57.941 34.615 16.11 0.00 40.50 3.18
3788 4634 8.525316 TCGAAATACTAGTATGAAGTGGTCAAA 58.475 33.333 16.11 0.00 40.50 2.69
3789 4635 8.592998 CGAAATACTAGTATGAAGTGGTCAAAC 58.407 37.037 16.11 0.00 40.50 2.93
3790 4636 9.431887 GAAATACTAGTATGAAGTGGTCAAACA 57.568 33.333 16.11 0.00 40.50 2.83
3791 4637 9.959721 AAATACTAGTATGAAGTGGTCAAACAT 57.040 29.630 16.11 0.00 40.50 2.71
3792 4638 8.948631 ATACTAGTATGAAGTGGTCAAACATG 57.051 34.615 14.71 0.00 40.50 3.21
3793 4639 5.643777 ACTAGTATGAAGTGGTCAAACATGC 59.356 40.000 0.00 0.00 40.50 4.06
3794 4640 4.397420 AGTATGAAGTGGTCAAACATGCA 58.603 39.130 0.00 0.00 40.50 3.96
3795 4641 4.826733 AGTATGAAGTGGTCAAACATGCAA 59.173 37.500 0.00 0.00 40.50 4.08
3796 4642 4.669206 ATGAAGTGGTCAAACATGCAAA 57.331 36.364 0.00 0.00 40.50 3.68
3797 4643 4.044336 TGAAGTGGTCAAACATGCAAAG 57.956 40.909 0.00 0.00 31.51 2.77
3798 4644 2.514205 AGTGGTCAAACATGCAAAGC 57.486 45.000 0.00 0.00 0.00 3.51
3799 4645 1.755959 AGTGGTCAAACATGCAAAGCA 59.244 42.857 0.00 0.00 44.86 3.91
3800 4646 1.860326 GTGGTCAAACATGCAAAGCAC 59.140 47.619 0.00 0.00 43.04 4.40
3801 4647 1.479730 TGGTCAAACATGCAAAGCACA 59.520 42.857 0.00 0.00 43.04 4.57
3802 4648 2.129607 GGTCAAACATGCAAAGCACAG 58.870 47.619 0.00 0.00 43.04 3.66
3803 4649 2.129607 GTCAAACATGCAAAGCACAGG 58.870 47.619 0.00 0.00 43.04 4.00
3804 4650 1.755959 TCAAACATGCAAAGCACAGGT 59.244 42.857 0.00 0.00 43.04 4.00
3805 4651 1.862201 CAAACATGCAAAGCACAGGTG 59.138 47.619 0.00 0.00 43.04 4.00
3806 4652 0.390124 AACATGCAAAGCACAGGTGG 59.610 50.000 1.10 0.00 43.04 4.61
3807 4653 0.756442 ACATGCAAAGCACAGGTGGT 60.756 50.000 0.00 0.00 43.04 4.16
3826 4672 2.612672 GGTTAGAACCGCAATAAGGAGC 59.387 50.000 0.00 0.00 39.66 4.70
3827 4673 3.267483 GTTAGAACCGCAATAAGGAGCA 58.733 45.455 0.00 0.00 0.00 4.26
3828 4674 2.717639 AGAACCGCAATAAGGAGCAT 57.282 45.000 0.00 0.00 0.00 3.79
3829 4675 2.292267 AGAACCGCAATAAGGAGCATG 58.708 47.619 0.00 0.00 0.00 4.06
3830 4676 2.092968 AGAACCGCAATAAGGAGCATGA 60.093 45.455 0.00 0.00 0.00 3.07
3831 4677 2.645838 ACCGCAATAAGGAGCATGAT 57.354 45.000 0.00 0.00 0.00 2.45
3832 4678 2.936202 ACCGCAATAAGGAGCATGATT 58.064 42.857 0.00 0.00 0.00 2.57
3833 4679 2.880890 ACCGCAATAAGGAGCATGATTC 59.119 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.843019 TCTGAGAAAATTACCCTGTCCTT 57.157 39.130 0.00 0.00 0.00 3.36
83 86 8.571461 TTGAAATCTTGAATTGTCTCATAGCT 57.429 30.769 0.00 0.00 0.00 3.32
147 150 2.940158 TCGAATCAGGGGAATAGTCGA 58.060 47.619 0.00 0.00 33.99 4.20
149 152 5.368989 ACAATTCGAATCAGGGGAATAGTC 58.631 41.667 11.83 0.00 30.63 2.59
205 208 8.693120 AGATACATGCTCATTGAAAGATTGAT 57.307 30.769 0.00 0.00 0.00 2.57
299 303 3.311322 TGGTTCAAGTTTCTGCTACAACG 59.689 43.478 0.00 0.00 0.00 4.10
356 370 6.839124 ATTGACATCAAAATGCTCCAGTTA 57.161 33.333 0.00 0.00 39.55 2.24
424 438 1.278985 ACTCTTCCATTGCCGATGACA 59.721 47.619 0.00 0.00 38.03 3.58
427 441 2.322355 AGACTCTTCCATTGCCGATG 57.678 50.000 0.00 0.00 35.42 3.84
428 442 2.766263 TGTAGACTCTTCCATTGCCGAT 59.234 45.455 0.00 0.00 0.00 4.18
493 514 6.481954 AGAATTTAACCTCAGTGCTTAACG 57.518 37.500 0.00 0.00 0.00 3.18
574 595 7.811282 ACTACCCCAAAACATATCATGACATA 58.189 34.615 0.00 0.00 0.00 2.29
662 685 0.956633 TTATCTAGTACAGCGGCGGG 59.043 55.000 9.78 0.00 0.00 6.13
712 739 3.214328 CCTGTTCGATTTGGGATTAGGG 58.786 50.000 0.00 0.00 0.00 3.53
763 798 0.818445 GGAGGAGGAGCGTATGACGA 60.818 60.000 2.65 0.00 46.05 4.20
1499 1536 3.877559 CTGATAGCACAAATCCTGGACA 58.122 45.455 0.00 0.00 0.00 4.02
1576 1613 1.862827 CAAAAGGCTTTGTGCTGCTTC 59.137 47.619 14.19 0.00 42.39 3.86
1891 2040 7.598869 GCATTACAGTGGAATACGATAATCTCA 59.401 37.037 0.00 0.00 0.00 3.27
2096 2344 6.423905 GTGATAGCTATTGCCGATTGAACTTA 59.576 38.462 7.87 0.00 40.80 2.24
2101 2349 4.335400 TGTGATAGCTATTGCCGATTGA 57.665 40.909 7.87 0.00 40.80 2.57
2128 2381 5.628797 ACAATTGGTTGGATTTTTGACCT 57.371 34.783 10.83 0.00 39.70 3.85
2129 2382 7.793927 TTAACAATTGGTTGGATTTTTGACC 57.206 32.000 10.83 0.00 40.73 4.02
2232 2485 5.888105 CCATAGAAATGGTTGAAGCTTCTG 58.112 41.667 26.09 11.66 46.68 3.02
2352 2769 7.670009 TTAGCAAGTAAAAATAACTACGCCA 57.330 32.000 0.00 0.00 0.00 5.69
2354 2771 9.550811 AACATTAGCAAGTAAAAATAACTACGC 57.449 29.630 0.00 0.00 0.00 4.42
2415 2832 5.102967 AGGGAGTAACATGTAACCCCTTTA 58.897 41.667 17.42 0.00 39.53 1.85
2582 2999 3.404869 AGTGATGATGTACTCCCTCCA 57.595 47.619 0.00 0.00 0.00 3.86
2598 3015 7.039722 ACCTATTCCCAATTTTCCTTAGTGA 57.960 36.000 0.00 0.00 0.00 3.41
2599 3016 7.547227 CAACCTATTCCCAATTTTCCTTAGTG 58.453 38.462 0.00 0.00 0.00 2.74
2600 3017 6.154534 GCAACCTATTCCCAATTTTCCTTAGT 59.845 38.462 0.00 0.00 0.00 2.24
2641 3058 1.405105 ACAAAGCACGCACTGTTCAAT 59.595 42.857 0.00 0.00 0.00 2.57
2643 3060 0.376852 GACAAAGCACGCACTGTTCA 59.623 50.000 0.00 0.00 0.00 3.18
2653 3070 2.095372 GGCTATTACACCGACAAAGCAC 59.905 50.000 0.00 0.00 0.00 4.40
2695 3112 3.894427 TCCTGCAAGCATAAAGGTTTCAA 59.106 39.130 0.00 0.00 35.33 2.69
2767 3184 0.323178 CCAACTCTGCATCAAGGCCT 60.323 55.000 0.00 0.00 0.00 5.19
2839 3256 3.253677 CCATCGGTAGCCTACAGTAGAAG 59.746 52.174 9.38 0.00 0.00 2.85
2852 3269 3.245797 CAGATCGCAATACCATCGGTAG 58.754 50.000 0.00 0.00 41.83 3.18
2856 3273 1.794701 CCACAGATCGCAATACCATCG 59.205 52.381 0.00 0.00 0.00 3.84
2862 3279 5.705441 AGTTTCTTTTCCACAGATCGCAATA 59.295 36.000 0.00 0.00 0.00 1.90
2904 3321 4.899502 AGGAGAAGGTTACAGTGACATTG 58.100 43.478 0.00 0.00 0.00 2.82
2907 3324 3.709653 ACAAGGAGAAGGTTACAGTGACA 59.290 43.478 0.00 0.00 0.00 3.58
2909 3326 5.104693 TGAAACAAGGAGAAGGTTACAGTGA 60.105 40.000 0.00 0.00 0.00 3.41
2910 3327 5.007724 GTGAAACAAGGAGAAGGTTACAGTG 59.992 44.000 0.00 0.00 36.32 3.66
2996 3413 0.257039 CCATCACAAAGGGGGAGGAG 59.743 60.000 0.00 0.00 0.00 3.69
3002 3419 2.324541 TCCAAAACCATCACAAAGGGG 58.675 47.619 0.00 0.00 0.00 4.79
3028 3445 9.880157 GTATTTTACACATCTTCAGGTACCTTA 57.120 33.333 13.15 0.20 0.00 2.69
3083 3827 8.854117 GCCCATATGAGATTTTCTAATCAGTTT 58.146 33.333 3.65 0.00 42.18 2.66
3104 3848 1.677633 GTACCGCCAGTTTGCCCAT 60.678 57.895 0.00 0.00 0.00 4.00
3106 3850 2.033602 AGTACCGCCAGTTTGCCC 59.966 61.111 0.00 0.00 0.00 5.36
3132 3876 5.351465 CGATGGACAATATAATGGTACTGCC 59.649 44.000 0.00 0.00 37.90 4.85
3265 4111 6.207691 GCAATGGCAAAATAAGTAAGAGGA 57.792 37.500 0.00 0.00 40.72 3.71
3298 4144 5.237996 TGCTCAAGAATCTTCAAGAGTTGTG 59.762 40.000 9.58 0.00 34.72 3.33
3299 4145 5.371526 TGCTCAAGAATCTTCAAGAGTTGT 58.628 37.500 9.58 0.00 34.72 3.32
3337 4183 9.888878 CATCTGAATTTCAAGCGATATTTACAT 57.111 29.630 0.01 0.00 0.00 2.29
3374 4220 7.879160 GGCTCTGAATCTCATCTCTGAATTAAT 59.121 37.037 0.00 0.00 0.00 1.40
3375 4221 7.147602 TGGCTCTGAATCTCATCTCTGAATTAA 60.148 37.037 0.00 0.00 0.00 1.40
3391 4237 3.110705 AGTACAGACCATGGCTCTGAAT 58.889 45.455 32.97 21.76 37.90 2.57
3397 4243 0.905357 GACCAGTACAGACCATGGCT 59.095 55.000 13.04 7.31 36.21 4.75
3401 4247 2.768527 CAGGATGACCAGTACAGACCAT 59.231 50.000 0.00 0.00 39.69 3.55
3405 4251 4.160329 AGAAACAGGATGACCAGTACAGA 58.840 43.478 0.00 0.00 39.69 3.41
3406 4252 4.021104 TGAGAAACAGGATGACCAGTACAG 60.021 45.833 0.00 0.00 39.69 2.74
3446 4292 7.699812 GGAAAGCATACTTCTGCAGAAAAATAG 59.300 37.037 28.16 18.98 44.77 1.73
3477 4323 5.293324 GGCATGATATTCGTAACTGACACAA 59.707 40.000 0.00 0.00 0.00 3.33
3546 4392 4.322123 GGGAACTAGCGAGTCTTTTTCTCT 60.322 45.833 0.00 0.00 33.58 3.10
3547 4393 3.927758 GGGAACTAGCGAGTCTTTTTCTC 59.072 47.826 0.00 0.00 33.58 2.87
3548 4394 3.579151 AGGGAACTAGCGAGTCTTTTTCT 59.421 43.478 0.00 0.00 40.61 2.52
3549 4395 3.927758 GAGGGAACTAGCGAGTCTTTTTC 59.072 47.826 0.00 0.00 44.43 2.29
3550 4396 3.579151 AGAGGGAACTAGCGAGTCTTTTT 59.421 43.478 0.00 0.00 44.43 1.94
3551 4397 3.056465 CAGAGGGAACTAGCGAGTCTTTT 60.056 47.826 0.00 0.00 44.43 2.27
3552 4398 2.494073 CAGAGGGAACTAGCGAGTCTTT 59.506 50.000 0.00 0.00 44.43 2.52
3553 4399 2.096248 CAGAGGGAACTAGCGAGTCTT 58.904 52.381 0.00 0.00 44.43 3.01
3554 4400 1.004979 ACAGAGGGAACTAGCGAGTCT 59.995 52.381 0.00 0.00 44.43 3.24
3555 4401 1.402613 GACAGAGGGAACTAGCGAGTC 59.597 57.143 0.00 0.00 44.43 3.36
3556 4402 1.465794 GACAGAGGGAACTAGCGAGT 58.534 55.000 0.00 0.00 44.43 4.18
3557 4403 0.741915 GGACAGAGGGAACTAGCGAG 59.258 60.000 0.00 0.00 44.43 5.03
3558 4404 0.039180 TGGACAGAGGGAACTAGCGA 59.961 55.000 0.00 0.00 44.43 4.93
3559 4405 0.895530 TTGGACAGAGGGAACTAGCG 59.104 55.000 0.00 0.00 44.43 4.26
3560 4406 1.623811 TGTTGGACAGAGGGAACTAGC 59.376 52.381 0.00 0.00 44.43 3.42
3572 4418 5.298989 AGGTTTACACATACTGTTGGACA 57.701 39.130 0.00 0.00 33.91 4.02
3573 4419 6.877322 ACATAGGTTTACACATACTGTTGGAC 59.123 38.462 0.00 0.00 33.91 4.02
3574 4420 7.011499 ACATAGGTTTACACATACTGTTGGA 57.989 36.000 0.00 0.00 33.91 3.53
3575 4421 6.035650 CGACATAGGTTTACACATACTGTTGG 59.964 42.308 0.00 0.00 33.91 3.77
3576 4422 6.035650 CCGACATAGGTTTACACATACTGTTG 59.964 42.308 0.00 0.00 33.91 3.33
3577 4423 6.103997 CCGACATAGGTTTACACATACTGTT 58.896 40.000 0.00 0.00 33.91 3.16
3578 4424 5.186409 ACCGACATAGGTTTACACATACTGT 59.814 40.000 0.00 0.00 43.00 3.55
3579 4425 5.657474 ACCGACATAGGTTTACACATACTG 58.343 41.667 0.00 0.00 43.00 2.74
3580 4426 5.927281 ACCGACATAGGTTTACACATACT 57.073 39.130 0.00 0.00 43.00 2.12
3591 4437 5.511716 TTTGTATCACACAACCGACATAGGT 60.512 40.000 0.00 0.00 46.80 3.08
3592 4438 4.118093 TGTATCACACAACCGACATAGG 57.882 45.455 0.00 0.00 32.95 2.57
3593 4439 6.662414 ATTTGTATCACACAACCGACATAG 57.338 37.500 0.00 0.00 46.80 2.23
3594 4440 8.549338 TTTATTTGTATCACACAACCGACATA 57.451 30.769 0.00 0.00 46.80 2.29
3595 4441 7.441890 TTTATTTGTATCACACAACCGACAT 57.558 32.000 0.00 0.00 46.80 3.06
3596 4442 6.862711 TTTATTTGTATCACACAACCGACA 57.137 33.333 0.00 0.00 46.80 4.35
3597 4443 9.433317 CATATTTATTTGTATCACACAACCGAC 57.567 33.333 0.00 0.00 46.80 4.79
3598 4444 9.384764 TCATATTTATTTGTATCACACAACCGA 57.615 29.630 0.00 0.00 46.80 4.69
3611 4457 9.450807 GCGCTTAAACAGATCATATTTATTTGT 57.549 29.630 0.00 0.00 0.00 2.83
3612 4458 9.669353 AGCGCTTAAACAGATCATATTTATTTG 57.331 29.630 2.64 0.00 0.00 2.32
3614 4460 9.669353 CAAGCGCTTAAACAGATCATATTTATT 57.331 29.630 24.55 0.00 0.00 1.40
3615 4461 8.840321 ACAAGCGCTTAAACAGATCATATTTAT 58.160 29.630 24.55 0.00 0.00 1.40
3616 4462 8.208718 ACAAGCGCTTAAACAGATCATATTTA 57.791 30.769 24.55 0.00 0.00 1.40
3617 4463 7.088589 ACAAGCGCTTAAACAGATCATATTT 57.911 32.000 24.55 0.00 0.00 1.40
3618 4464 6.316140 TGACAAGCGCTTAAACAGATCATATT 59.684 34.615 24.55 0.00 0.00 1.28
3619 4465 5.817296 TGACAAGCGCTTAAACAGATCATAT 59.183 36.000 24.55 0.00 0.00 1.78
3620 4466 5.175127 TGACAAGCGCTTAAACAGATCATA 58.825 37.500 24.55 0.00 0.00 2.15
3621 4467 4.002982 TGACAAGCGCTTAAACAGATCAT 58.997 39.130 24.55 0.00 0.00 2.45
3622 4468 3.398406 TGACAAGCGCTTAAACAGATCA 58.602 40.909 24.55 14.06 0.00 2.92
3623 4469 4.404507 TTGACAAGCGCTTAAACAGATC 57.595 40.909 24.55 11.76 0.00 2.75
3624 4470 5.156355 CAATTGACAAGCGCTTAAACAGAT 58.844 37.500 24.55 14.39 0.00 2.90
3625 4471 4.036262 ACAATTGACAAGCGCTTAAACAGA 59.964 37.500 24.55 13.01 0.00 3.41
3626 4472 4.290155 ACAATTGACAAGCGCTTAAACAG 58.710 39.130 24.55 12.78 0.00 3.16
3627 4473 4.300189 ACAATTGACAAGCGCTTAAACA 57.700 36.364 24.55 19.02 0.00 2.83
3628 4474 5.225129 CGATACAATTGACAAGCGCTTAAAC 59.775 40.000 24.55 16.67 0.00 2.01
3629 4475 5.120986 TCGATACAATTGACAAGCGCTTAAA 59.879 36.000 24.55 17.46 0.00 1.52
3630 4476 4.627900 TCGATACAATTGACAAGCGCTTAA 59.372 37.500 24.55 14.57 0.00 1.85
3631 4477 4.177783 TCGATACAATTGACAAGCGCTTA 58.822 39.130 24.55 7.71 0.00 3.09
3632 4478 3.000041 TCGATACAATTGACAAGCGCTT 59.000 40.909 18.98 18.98 0.00 4.68
3633 4479 2.616960 TCGATACAATTGACAAGCGCT 58.383 42.857 13.59 2.64 0.00 5.92
3634 4480 3.592381 ATCGATACAATTGACAAGCGC 57.408 42.857 13.59 0.00 0.00 5.92
3635 4481 4.518217 GGAATCGATACAATTGACAAGCG 58.482 43.478 13.59 11.45 0.00 4.68
3636 4482 4.034048 ACGGAATCGATACAATTGACAAGC 59.966 41.667 13.59 0.00 40.11 4.01
3637 4483 5.718649 ACGGAATCGATACAATTGACAAG 57.281 39.130 13.59 1.05 40.11 3.16
3638 4484 6.981559 TGATACGGAATCGATACAATTGACAA 59.018 34.615 13.59 0.00 37.42 3.18
3639 4485 6.508777 TGATACGGAATCGATACAATTGACA 58.491 36.000 13.59 0.00 37.42 3.58
3640 4486 6.861572 TCTGATACGGAATCGATACAATTGAC 59.138 38.462 13.59 2.42 37.42 3.18
3641 4487 6.977213 TCTGATACGGAATCGATACAATTGA 58.023 36.000 13.59 0.00 37.42 2.57
3642 4488 7.818493 ATCTGATACGGAATCGATACAATTG 57.182 36.000 3.24 3.24 37.42 2.32
3644 4490 9.737427 GATTATCTGATACGGAATCGATACAAT 57.263 33.333 0.00 0.00 37.42 2.71
3645 4491 8.188799 GGATTATCTGATACGGAATCGATACAA 58.811 37.037 0.00 0.00 37.42 2.41
3646 4492 7.338449 TGGATTATCTGATACGGAATCGATACA 59.662 37.037 0.00 0.00 37.42 2.29
3647 4493 7.644551 GTGGATTATCTGATACGGAATCGATAC 59.355 40.741 0.00 0.00 37.42 2.24
3648 4494 7.338449 TGTGGATTATCTGATACGGAATCGATA 59.662 37.037 0.00 0.00 37.42 2.92
3649 4495 6.152831 TGTGGATTATCTGATACGGAATCGAT 59.847 38.462 0.00 0.00 37.42 3.59
3650 4496 5.475564 TGTGGATTATCTGATACGGAATCGA 59.524 40.000 0.00 0.00 37.42 3.59
3651 4497 5.709966 TGTGGATTATCTGATACGGAATCG 58.290 41.667 0.00 0.00 37.42 3.34
3668 4514 9.835389 CAACAATTTTCCCAATTATATGTGGAT 57.165 29.630 4.17 0.00 37.03 3.41
3669 4515 9.040259 TCAACAATTTTCCCAATTATATGTGGA 57.960 29.630 4.17 0.00 37.03 4.02
3670 4516 9.835389 ATCAACAATTTTCCCAATTATATGTGG 57.165 29.630 0.00 0.00 34.44 4.17
3679 4525 9.187996 ACTTTCAAAATCAACAATTTTCCCAAT 57.812 25.926 0.00 0.00 44.04 3.16
3680 4526 8.572855 ACTTTCAAAATCAACAATTTTCCCAA 57.427 26.923 0.00 0.00 44.04 4.12
3681 4527 8.457261 CAACTTTCAAAATCAACAATTTTCCCA 58.543 29.630 0.00 0.00 44.04 4.37
3682 4528 8.458052 ACAACTTTCAAAATCAACAATTTTCCC 58.542 29.630 0.00 0.00 44.04 3.97
3683 4529 9.276397 CACAACTTTCAAAATCAACAATTTTCC 57.724 29.630 0.00 0.00 44.04 3.13
3684 4530 9.824534 ACACAACTTTCAAAATCAACAATTTTC 57.175 25.926 0.00 0.00 44.04 2.29
3687 4533 9.097257 CCTACACAACTTTCAAAATCAACAATT 57.903 29.630 0.00 0.00 0.00 2.32
3688 4534 8.257306 ACCTACACAACTTTCAAAATCAACAAT 58.743 29.630 0.00 0.00 0.00 2.71
3689 4535 7.543868 CACCTACACAACTTTCAAAATCAACAA 59.456 33.333 0.00 0.00 0.00 2.83
3690 4536 7.032580 CACCTACACAACTTTCAAAATCAACA 58.967 34.615 0.00 0.00 0.00 3.33
3691 4537 7.033185 ACACCTACACAACTTTCAAAATCAAC 58.967 34.615 0.00 0.00 0.00 3.18
3692 4538 7.164230 ACACCTACACAACTTTCAAAATCAA 57.836 32.000 0.00 0.00 0.00 2.57
3693 4539 6.767524 ACACCTACACAACTTTCAAAATCA 57.232 33.333 0.00 0.00 0.00 2.57
3694 4540 7.033185 ACAACACCTACACAACTTTCAAAATC 58.967 34.615 0.00 0.00 0.00 2.17
3695 4541 6.930731 ACAACACCTACACAACTTTCAAAAT 58.069 32.000 0.00 0.00 0.00 1.82
3696 4542 6.334102 ACAACACCTACACAACTTTCAAAA 57.666 33.333 0.00 0.00 0.00 2.44
3697 4543 5.968528 ACAACACCTACACAACTTTCAAA 57.031 34.783 0.00 0.00 0.00 2.69
3698 4544 7.633193 AATACAACACCTACACAACTTTCAA 57.367 32.000 0.00 0.00 0.00 2.69
3699 4545 7.554835 AGAAATACAACACCTACACAACTTTCA 59.445 33.333 0.00 0.00 0.00 2.69
3700 4546 7.855904 CAGAAATACAACACCTACACAACTTTC 59.144 37.037 0.00 0.00 0.00 2.62
3701 4547 7.201785 CCAGAAATACAACACCTACACAACTTT 60.202 37.037 0.00 0.00 0.00 2.66
3702 4548 6.262273 CCAGAAATACAACACCTACACAACTT 59.738 38.462 0.00 0.00 0.00 2.66
3703 4549 5.763204 CCAGAAATACAACACCTACACAACT 59.237 40.000 0.00 0.00 0.00 3.16
3704 4550 5.529800 ACCAGAAATACAACACCTACACAAC 59.470 40.000 0.00 0.00 0.00 3.32
3705 4551 5.686753 ACCAGAAATACAACACCTACACAA 58.313 37.500 0.00 0.00 0.00 3.33
3706 4552 5.298989 ACCAGAAATACAACACCTACACA 57.701 39.130 0.00 0.00 0.00 3.72
3707 4553 4.387862 CGACCAGAAATACAACACCTACAC 59.612 45.833 0.00 0.00 0.00 2.90
3708 4554 4.281435 TCGACCAGAAATACAACACCTACA 59.719 41.667 0.00 0.00 0.00 2.74
3709 4555 4.813027 TCGACCAGAAATACAACACCTAC 58.187 43.478 0.00 0.00 0.00 3.18
3710 4556 5.471556 TTCGACCAGAAATACAACACCTA 57.528 39.130 0.00 0.00 35.61 3.08
3711 4557 4.345859 TTCGACCAGAAATACAACACCT 57.654 40.909 0.00 0.00 35.61 4.00
3712 4558 4.083484 CCTTTCGACCAGAAATACAACACC 60.083 45.833 0.00 0.00 46.60 4.16
3713 4559 4.753107 TCCTTTCGACCAGAAATACAACAC 59.247 41.667 0.00 0.00 46.60 3.32
3714 4560 4.963373 TCCTTTCGACCAGAAATACAACA 58.037 39.130 0.00 0.00 46.60 3.33
3715 4561 4.995487 ACTCCTTTCGACCAGAAATACAAC 59.005 41.667 0.00 0.00 46.60 3.32
3716 4562 5.223449 ACTCCTTTCGACCAGAAATACAA 57.777 39.130 0.00 0.00 46.60 2.41
3717 4563 4.884668 ACTCCTTTCGACCAGAAATACA 57.115 40.909 0.00 0.00 46.60 2.29
3718 4564 4.797349 CGTACTCCTTTCGACCAGAAATAC 59.203 45.833 0.00 0.00 46.60 1.89
3719 4565 4.142315 CCGTACTCCTTTCGACCAGAAATA 60.142 45.833 0.00 0.00 46.60 1.40
3720 4566 3.368116 CCGTACTCCTTTCGACCAGAAAT 60.368 47.826 0.00 0.00 46.60 2.17
3721 4567 2.029649 CCGTACTCCTTTCGACCAGAAA 60.030 50.000 0.00 0.00 45.76 2.52
3722 4568 1.542915 CCGTACTCCTTTCGACCAGAA 59.457 52.381 0.00 0.00 37.01 3.02
3723 4569 1.171308 CCGTACTCCTTTCGACCAGA 58.829 55.000 0.00 0.00 0.00 3.86
3724 4570 0.458025 GCCGTACTCCTTTCGACCAG 60.458 60.000 0.00 0.00 0.00 4.00
3725 4571 1.180456 TGCCGTACTCCTTTCGACCA 61.180 55.000 0.00 0.00 0.00 4.02
3726 4572 0.735287 GTGCCGTACTCCTTTCGACC 60.735 60.000 0.00 0.00 0.00 4.79
3727 4573 0.243095 AGTGCCGTACTCCTTTCGAC 59.757 55.000 0.00 0.00 33.17 4.20
3728 4574 2.649831 AGTGCCGTACTCCTTTCGA 58.350 52.632 0.00 0.00 33.17 3.71
3736 4582 2.185004 AAAATGCAGAGTGCCGTACT 57.815 45.000 0.00 0.00 44.23 2.73
3737 4583 2.989422 AAAAATGCAGAGTGCCGTAC 57.011 45.000 0.00 0.00 44.23 3.67
3756 4602 8.121086 CACTTCATACTAGTATTTCGAGACGAA 58.879 37.037 12.87 9.56 44.28 3.85
3757 4603 7.254692 CCACTTCATACTAGTATTTCGAGACGA 60.255 40.741 12.87 2.29 0.00 4.20
3758 4604 6.851837 CCACTTCATACTAGTATTTCGAGACG 59.148 42.308 12.87 7.25 0.00 4.18
3759 4605 7.705214 ACCACTTCATACTAGTATTTCGAGAC 58.295 38.462 12.87 0.00 0.00 3.36
3760 4606 7.555195 TGACCACTTCATACTAGTATTTCGAGA 59.445 37.037 12.87 4.38 0.00 4.04
3761 4607 7.704271 TGACCACTTCATACTAGTATTTCGAG 58.296 38.462 12.87 10.33 0.00 4.04
3762 4608 7.634671 TGACCACTTCATACTAGTATTTCGA 57.365 36.000 12.87 5.09 0.00 3.71
3763 4609 8.592998 GTTTGACCACTTCATACTAGTATTTCG 58.407 37.037 12.87 6.59 34.32 3.46
3764 4610 9.431887 TGTTTGACCACTTCATACTAGTATTTC 57.568 33.333 12.87 2.63 37.16 2.17
3765 4611 9.959721 ATGTTTGACCACTTCATACTAGTATTT 57.040 29.630 12.87 0.00 37.16 1.40
3766 4612 9.383519 CATGTTTGACCACTTCATACTAGTATT 57.616 33.333 12.87 0.00 37.16 1.89
3767 4613 7.495934 GCATGTTTGACCACTTCATACTAGTAT 59.504 37.037 9.71 9.71 37.16 2.12
3768 4614 6.816640 GCATGTTTGACCACTTCATACTAGTA 59.183 38.462 4.77 4.77 37.16 1.82
3769 4615 5.643777 GCATGTTTGACCACTTCATACTAGT 59.356 40.000 0.00 0.00 37.16 2.57
3770 4616 5.643348 TGCATGTTTGACCACTTCATACTAG 59.357 40.000 0.00 0.00 37.16 2.57
3771 4617 5.555966 TGCATGTTTGACCACTTCATACTA 58.444 37.500 0.00 0.00 37.16 1.82
3772 4618 4.397420 TGCATGTTTGACCACTTCATACT 58.603 39.130 0.00 0.00 37.16 2.12
3773 4619 4.764679 TGCATGTTTGACCACTTCATAC 57.235 40.909 0.00 0.00 36.86 2.39
3774 4620 5.771469 CTTTGCATGTTTGACCACTTCATA 58.229 37.500 0.00 0.00 32.84 2.15
3775 4621 4.624015 CTTTGCATGTTTGACCACTTCAT 58.376 39.130 0.00 0.00 32.84 2.57
3776 4622 3.737663 GCTTTGCATGTTTGACCACTTCA 60.738 43.478 0.00 0.00 0.00 3.02
3777 4623 2.796593 GCTTTGCATGTTTGACCACTTC 59.203 45.455 0.00 0.00 0.00 3.01
3778 4624 2.168106 TGCTTTGCATGTTTGACCACTT 59.832 40.909 0.00 0.00 31.71 3.16
3779 4625 1.755959 TGCTTTGCATGTTTGACCACT 59.244 42.857 0.00 0.00 31.71 4.00
3780 4626 1.860326 GTGCTTTGCATGTTTGACCAC 59.140 47.619 0.00 0.00 41.91 4.16
3781 4627 1.479730 TGTGCTTTGCATGTTTGACCA 59.520 42.857 0.00 0.00 41.91 4.02
3782 4628 2.129607 CTGTGCTTTGCATGTTTGACC 58.870 47.619 0.00 0.00 41.91 4.02
3783 4629 2.129607 CCTGTGCTTTGCATGTTTGAC 58.870 47.619 0.00 0.00 41.91 3.18
3784 4630 1.755959 ACCTGTGCTTTGCATGTTTGA 59.244 42.857 0.00 0.00 41.91 2.69
3785 4631 1.862201 CACCTGTGCTTTGCATGTTTG 59.138 47.619 0.00 0.00 41.91 2.93
3786 4632 1.202557 CCACCTGTGCTTTGCATGTTT 60.203 47.619 0.00 0.00 41.91 2.83
3787 4633 0.390124 CCACCTGTGCTTTGCATGTT 59.610 50.000 0.00 0.00 41.91 2.71
3788 4634 0.756442 ACCACCTGTGCTTTGCATGT 60.756 50.000 0.00 0.00 41.91 3.21
3789 4635 0.390124 AACCACCTGTGCTTTGCATG 59.610 50.000 0.00 0.00 41.91 4.06
3790 4636 1.888512 CTAACCACCTGTGCTTTGCAT 59.111 47.619 0.00 0.00 41.91 3.96
3791 4637 1.133945 TCTAACCACCTGTGCTTTGCA 60.134 47.619 0.00 0.00 35.60 4.08
3792 4638 1.604604 TCTAACCACCTGTGCTTTGC 58.395 50.000 0.00 0.00 0.00 3.68
3793 4639 3.626028 GTTCTAACCACCTGTGCTTTG 57.374 47.619 0.00 0.00 0.00 2.77
3805 4651 2.612672 GCTCCTTATTGCGGTTCTAACC 59.387 50.000 1.54 1.54 45.76 2.85
3806 4652 3.267483 TGCTCCTTATTGCGGTTCTAAC 58.733 45.455 0.00 0.00 0.00 2.34
3807 4653 3.620427 TGCTCCTTATTGCGGTTCTAA 57.380 42.857 0.00 0.00 0.00 2.10
3808 4654 3.133901 TCATGCTCCTTATTGCGGTTCTA 59.866 43.478 0.00 0.00 0.00 2.10
3809 4655 2.092968 TCATGCTCCTTATTGCGGTTCT 60.093 45.455 0.00 0.00 0.00 3.01
3810 4656 2.288666 TCATGCTCCTTATTGCGGTTC 58.711 47.619 0.00 0.00 0.00 3.62
3811 4657 2.418368 TCATGCTCCTTATTGCGGTT 57.582 45.000 0.00 0.00 0.00 4.44
3812 4658 2.645838 ATCATGCTCCTTATTGCGGT 57.354 45.000 0.00 0.00 0.00 5.68
3813 4659 3.549299 GAATCATGCTCCTTATTGCGG 57.451 47.619 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.