Multiple sequence alignment - TraesCS3A01G014900

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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 TraesCS3A01G014900 chr3A 100.000 6410 0 0 1 6410 10212425 10218834 0.000000e+00 11838.0
1 TraesCS3A01G014900 chr3A 89.831 708 50 11 4927 5626 10577905 10577212 0.000000e+00 889.0
2 TraesCS3A01G014900 chr3A 76.923 1443 250 54 3611 5002 9853976 9855386 0.000000e+00 743.0
3 TraesCS3A01G014900 chr3A 92.443 397 29 1 4418 4814 10578344 10577949 3.350000e-157 566.0
4 TraesCS3A01G014900 chr3A 78.480 855 154 18 4576 5422 9933588 9934420 3.400000e-147 532.0
5 TraesCS3A01G014900 chr3A 79.826 461 65 10 859 1315 10165989 10166425 1.740000e-80 311.0
6 TraesCS3A01G014900 chr3A 80.997 321 36 16 1001 1315 9931696 9931997 1.390000e-56 231.0
7 TraesCS3A01G014900 chr3D 96.603 5946 154 24 471 6403 4404395 4410305 0.000000e+00 9817.0
8 TraesCS3A01G014900 chr3D 76.466 1432 251 57 3621 5002 4194521 4195916 0.000000e+00 699.0
9 TraesCS3A01G014900 chr3D 93.048 187 8 2 78 262 4404182 4404365 1.060000e-67 268.0
10 TraesCS3A01G014900 chr3D 86.957 92 4 1 1 92 4403624 4403707 5.290000e-16 97.1
11 TraesCS3A01G014900 chrUn 75.196 1782 347 72 3613 5353 35374067 35372340 0.000000e+00 754.0
12 TraesCS3A01G014900 chr3B 75.196 1782 347 72 3613 5353 6556989 6558716 0.000000e+00 754.0
13 TraesCS3A01G014900 chr3B 75.440 1535 290 58 3608 5090 6679120 6680619 0.000000e+00 665.0
14 TraesCS3A01G014900 chr3B 85.849 318 39 5 1001 1315 6677121 6677435 3.700000e-87 333.0
15 TraesCS3A01G014900 chr3B 90.411 146 14 0 327 472 368154355 368154210 6.560000e-45 193.0
16 TraesCS3A01G014900 chr3B 89.041 146 16 0 325 470 389769427 389769572 1.420000e-41 182.0
17 TraesCS3A01G014900 chr7D 78.581 747 122 32 3618 4341 499886347 499887078 5.860000e-125 459.0
18 TraesCS3A01G014900 chr7D 95.172 145 7 0 327 471 53753006 53753150 5.000000e-56 230.0
19 TraesCS3A01G014900 chr7A 77.520 734 125 30 3618 4330 565799060 565799774 7.740000e-109 405.0
20 TraesCS3A01G014900 chr6D 92.715 151 9 1 320 470 410151148 410151296 3.890000e-52 217.0
21 TraesCS3A01G014900 chr1A 91.034 145 13 0 327 471 49289338 49289482 5.070000e-46 196.0
22 TraesCS3A01G014900 chr7B 83.696 184 26 4 4149 4330 527858605 527858786 3.070000e-38 171.0
23 TraesCS3A01G014900 chr4A 93.333 105 5 1 365 469 276913981 276914083 3.090000e-33 154.0


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 TraesCS3A01G014900 chr3A 10212425 10218834 6409 False 11838.000000 11838 100.000000 1 6410 1 chr3A.!!$F3 6409
1 TraesCS3A01G014900 chr3A 9853976 9855386 1410 False 743.000000 743 76.923000 3611 5002 1 chr3A.!!$F1 1391
2 TraesCS3A01G014900 chr3A 10577212 10578344 1132 True 727.500000 889 91.137000 4418 5626 2 chr3A.!!$R1 1208
3 TraesCS3A01G014900 chr3A 9931696 9934420 2724 False 381.500000 532 79.738500 1001 5422 2 chr3A.!!$F4 4421
4 TraesCS3A01G014900 chr3D 4403624 4410305 6681 False 3394.033333 9817 92.202667 1 6403 3 chr3D.!!$F2 6402
5 TraesCS3A01G014900 chr3D 4194521 4195916 1395 False 699.000000 699 76.466000 3621 5002 1 chr3D.!!$F1 1381
6 TraesCS3A01G014900 chrUn 35372340 35374067 1727 True 754.000000 754 75.196000 3613 5353 1 chrUn.!!$R1 1740
7 TraesCS3A01G014900 chr3B 6556989 6558716 1727 False 754.000000 754 75.196000 3613 5353 1 chr3B.!!$F1 1740
8 TraesCS3A01G014900 chr3B 6677121 6680619 3498 False 499.000000 665 80.644500 1001 5090 2 chr3B.!!$F3 4089
9 TraesCS3A01G014900 chr7D 499886347 499887078 731 False 459.000000 459 78.581000 3618 4341 1 chr7D.!!$F2 723
10 TraesCS3A01G014900 chr7A 565799060 565799774 714 False 405.000000 405 77.520000 3618 4330 1 chr7A.!!$F1 712

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
441 933 0.169672 ATCGTACCGAGTGTTGGACG 59.830 55.000 0.00 0.0 39.91 4.79 F
1619 2183 0.101219 GGATGGCGCTCACCAATTTC 59.899 55.000 7.64 0.0 44.65 2.17 F
1621 2185 0.676466 ATGGCGCTCACCAATTTCGA 60.676 50.000 7.64 0.0 44.65 3.71 F
1817 2604 1.888512 CCATGCTGCAACCTAAACACT 59.111 47.619 6.36 0.0 0.00 3.55 F
2559 3375 0.911769 TGGTCCTCCCTTATGCACAG 59.088 55.000 0.00 0.0 0.00 3.66 F
3476 4698 1.148273 ACGCCACATGTCACCACTT 59.852 52.632 0.00 0.0 0.00 3.16 F
3522 4744 1.787012 GCATGCCACCACTTTTCAAG 58.213 50.000 6.36 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 3232 1.203287 GCTAAACCCCGTCGACTAGTT 59.797 52.381 14.70 11.02 0.00 2.24 R
2426 3242 1.334160 AAAACCTTGGCTAAACCCCG 58.666 50.000 0.00 0.00 37.83 5.73 R
2542 3358 2.237392 AGAACTGTGCATAAGGGAGGAC 59.763 50.000 0.00 0.00 0.00 3.85 R
3286 4507 2.627863 TTCCAAATTGATTCCGTGCG 57.372 45.000 0.00 0.00 0.00 5.34 R
3999 5260 1.003545 CACAACCTTGTCAGTTGAGCG 60.004 52.381 10.38 0.00 46.03 5.03 R
4725 6087 1.241165 TGTCGAAGAAGTAGCGGTGA 58.759 50.000 0.00 0.00 39.69 4.02 R
5662 7071 1.068885 GTAGATCGGAGTCTCATGGCG 60.069 57.143 1.47 0.00 0.00 5.69 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
21 22 1.623811 TCAGTTGTACTGGCCTTCTCC 59.376 52.381 3.32 0.00 45.94 3.71
35 36 4.202151 GGCCTTCTCCGATTTTAATTGCAT 60.202 41.667 0.00 0.00 0.00 3.96
49 50 2.936919 TTGCATGTCAGGAACACTCT 57.063 45.000 0.00 0.00 41.75 3.24
50 51 2.174363 TGCATGTCAGGAACACTCTG 57.826 50.000 0.00 0.00 41.75 3.35
51 52 1.271001 TGCATGTCAGGAACACTCTGG 60.271 52.381 0.00 0.00 41.75 3.86
52 53 1.002430 GCATGTCAGGAACACTCTGGA 59.998 52.381 0.00 0.00 41.75 3.86
53 54 2.550855 GCATGTCAGGAACACTCTGGAA 60.551 50.000 0.00 0.00 41.75 3.53
54 55 3.332919 CATGTCAGGAACACTCTGGAAG 58.667 50.000 0.00 0.00 41.75 3.46
55 56 2.398588 TGTCAGGAACACTCTGGAAGT 58.601 47.619 0.00 0.00 39.44 3.01
56 57 2.771943 TGTCAGGAACACTCTGGAAGTT 59.228 45.455 0.00 0.00 35.45 2.66
92 93 1.078497 CAGCATGCCACGGGAGTTA 60.078 57.895 15.66 0.00 44.67 2.24
93 94 0.676466 CAGCATGCCACGGGAGTTAA 60.676 55.000 15.66 0.00 44.67 2.01
95 96 0.958382 GCATGCCACGGGAGTTAACA 60.958 55.000 6.36 0.00 44.67 2.41
96 97 0.802494 CATGCCACGGGAGTTAACAC 59.198 55.000 8.61 0.73 44.67 3.32
135 627 2.943033 CCATCCTTTTTGGTACGGCTAG 59.057 50.000 0.00 0.00 37.07 3.42
144 636 1.770658 TGGTACGGCTAGCTAGGACTA 59.229 52.381 22.10 11.06 0.00 2.59
146 638 3.217626 GGTACGGCTAGCTAGGACTAAA 58.782 50.000 22.10 0.00 0.00 1.85
179 671 6.935240 TGTACCCTCTTCCCTATTGATATG 57.065 41.667 0.00 0.00 0.00 1.78
180 672 6.630131 TGTACCCTCTTCCCTATTGATATGA 58.370 40.000 0.00 0.00 0.00 2.15
181 673 6.497259 TGTACCCTCTTCCCTATTGATATGAC 59.503 42.308 0.00 0.00 0.00 3.06
220 712 3.765968 AACTGGTGGTTGGGGAATC 57.234 52.632 0.00 0.00 36.70 2.52
236 728 5.163237 TGGGGAATCTACTTTTAGGAATCCG 60.163 44.000 0.00 0.00 0.00 4.18
257 749 7.753309 TCCGAATGGTTTCTTTCAGAATTTA 57.247 32.000 0.00 0.00 33.67 1.40
308 800 2.688958 AGACTCGTTCTTCCTATTCCCG 59.311 50.000 0.00 0.00 0.00 5.14
310 802 2.688958 ACTCGTTCTTCCTATTCCCGAG 59.311 50.000 0.00 0.00 44.18 4.63
311 803 1.407979 TCGTTCTTCCTATTCCCGAGC 59.592 52.381 0.00 0.00 0.00 5.03
312 804 1.409427 CGTTCTTCCTATTCCCGAGCT 59.591 52.381 0.00 0.00 0.00 4.09
313 805 2.799917 CGTTCTTCCTATTCCCGAGCTG 60.800 54.545 0.00 0.00 0.00 4.24
314 806 2.431057 GTTCTTCCTATTCCCGAGCTGA 59.569 50.000 0.00 0.00 0.00 4.26
315 807 2.964209 TCTTCCTATTCCCGAGCTGAT 58.036 47.619 0.00 0.00 0.00 2.90
316 808 4.114015 TCTTCCTATTCCCGAGCTGATA 57.886 45.455 0.00 0.00 0.00 2.15
317 809 4.678256 TCTTCCTATTCCCGAGCTGATAT 58.322 43.478 0.00 0.00 0.00 1.63
318 810 4.464244 TCTTCCTATTCCCGAGCTGATATG 59.536 45.833 0.00 0.00 0.00 1.78
319 811 3.099905 TCCTATTCCCGAGCTGATATGG 58.900 50.000 0.00 0.00 0.00 2.74
320 812 2.419297 CCTATTCCCGAGCTGATATGGC 60.419 54.545 0.00 0.00 0.00 4.40
321 813 1.059098 ATTCCCGAGCTGATATGGCA 58.941 50.000 0.00 0.00 0.00 4.92
322 814 0.836606 TTCCCGAGCTGATATGGCAA 59.163 50.000 0.00 0.00 0.00 4.52
323 815 1.059098 TCCCGAGCTGATATGGCAAT 58.941 50.000 0.00 0.00 0.00 3.56
324 816 1.002430 TCCCGAGCTGATATGGCAATC 59.998 52.381 0.00 0.00 0.00 2.67
325 817 1.073964 CCGAGCTGATATGGCAATCG 58.926 55.000 0.00 0.00 0.00 3.34
326 818 1.337167 CCGAGCTGATATGGCAATCGA 60.337 52.381 0.00 0.00 32.11 3.59
327 819 2.407090 CGAGCTGATATGGCAATCGAA 58.593 47.619 0.00 0.00 32.11 3.71
328 820 2.802247 CGAGCTGATATGGCAATCGAAA 59.198 45.455 0.00 0.00 32.11 3.46
329 821 3.363378 CGAGCTGATATGGCAATCGAAAC 60.363 47.826 0.00 0.00 32.11 2.78
330 822 3.812053 GAGCTGATATGGCAATCGAAACT 59.188 43.478 0.00 0.00 0.00 2.66
331 823 3.562973 AGCTGATATGGCAATCGAAACTG 59.437 43.478 0.00 0.00 0.00 3.16
332 824 3.851105 GCTGATATGGCAATCGAAACTGC 60.851 47.826 8.55 8.55 37.86 4.40
333 825 3.544684 TGATATGGCAATCGAAACTGCT 58.455 40.909 14.71 2.27 38.65 4.24
334 826 3.561310 TGATATGGCAATCGAAACTGCTC 59.439 43.478 14.71 7.24 38.65 4.26
335 827 2.119801 ATGGCAATCGAAACTGCTCT 57.880 45.000 14.71 3.22 38.65 4.09
336 828 2.760634 TGGCAATCGAAACTGCTCTA 57.239 45.000 14.71 2.93 38.65 2.43
337 829 2.346803 TGGCAATCGAAACTGCTCTAC 58.653 47.619 14.71 2.41 38.65 2.59
338 830 1.324736 GGCAATCGAAACTGCTCTACG 59.675 52.381 14.71 0.00 38.65 3.51
339 831 1.993370 GCAATCGAAACTGCTCTACGT 59.007 47.619 9.53 0.00 35.62 3.57
340 832 3.176708 GCAATCGAAACTGCTCTACGTA 58.823 45.455 9.53 0.00 35.62 3.57
341 833 3.000971 GCAATCGAAACTGCTCTACGTAC 60.001 47.826 9.53 0.00 35.62 3.67
342 834 2.515641 TCGAAACTGCTCTACGTACG 57.484 50.000 15.01 15.01 0.00 3.67
343 835 2.068519 TCGAAACTGCTCTACGTACGA 58.931 47.619 24.41 4.69 0.00 3.43
344 836 2.674852 TCGAAACTGCTCTACGTACGAT 59.325 45.455 24.41 8.93 0.00 3.73
345 837 3.125829 TCGAAACTGCTCTACGTACGATT 59.874 43.478 24.41 2.35 0.00 3.34
346 838 3.477802 CGAAACTGCTCTACGTACGATTC 59.522 47.826 24.41 9.97 0.00 2.52
347 839 4.660105 GAAACTGCTCTACGTACGATTCT 58.340 43.478 24.41 1.05 0.00 2.40
348 840 4.698583 AACTGCTCTACGTACGATTCTT 57.301 40.909 24.41 0.61 0.00 2.52
349 841 4.698583 ACTGCTCTACGTACGATTCTTT 57.301 40.909 24.41 0.00 0.00 2.52
350 842 5.056894 ACTGCTCTACGTACGATTCTTTT 57.943 39.130 24.41 0.00 0.00 2.27
351 843 5.467705 ACTGCTCTACGTACGATTCTTTTT 58.532 37.500 24.41 0.00 0.00 1.94
381 873 1.694844 TGGTACGACCAGACAACAGA 58.305 50.000 3.02 0.00 44.79 3.41
382 874 2.244695 TGGTACGACCAGACAACAGAT 58.755 47.619 3.02 0.00 44.79 2.90
383 875 2.029380 TGGTACGACCAGACAACAGATG 60.029 50.000 3.02 0.00 44.79 2.90
384 876 1.993370 GTACGACCAGACAACAGATGC 59.007 52.381 0.00 0.00 0.00 3.91
385 877 0.681733 ACGACCAGACAACAGATGCT 59.318 50.000 0.00 0.00 0.00 3.79
386 878 1.893137 ACGACCAGACAACAGATGCTA 59.107 47.619 0.00 0.00 0.00 3.49
387 879 2.497675 ACGACCAGACAACAGATGCTAT 59.502 45.455 0.00 0.00 0.00 2.97
388 880 2.862536 CGACCAGACAACAGATGCTATG 59.137 50.000 0.00 0.00 0.00 2.23
389 881 3.201290 GACCAGACAACAGATGCTATGG 58.799 50.000 0.00 0.00 31.71 2.74
390 882 1.945394 CCAGACAACAGATGCTATGGC 59.055 52.381 0.00 0.00 39.26 4.40
391 883 1.945394 CAGACAACAGATGCTATGGCC 59.055 52.381 0.00 0.00 37.74 5.36
392 884 1.133976 AGACAACAGATGCTATGGCCC 60.134 52.381 0.00 0.00 37.74 5.80
393 885 0.625316 ACAACAGATGCTATGGCCCA 59.375 50.000 0.00 0.00 37.74 5.36
394 886 1.315690 CAACAGATGCTATGGCCCAG 58.684 55.000 0.00 0.00 37.74 4.45
395 887 1.134007 CAACAGATGCTATGGCCCAGA 60.134 52.381 0.00 0.00 37.74 3.86
396 888 1.216064 ACAGATGCTATGGCCCAGAA 58.784 50.000 0.00 0.00 37.74 3.02
397 889 1.565759 ACAGATGCTATGGCCCAGAAA 59.434 47.619 0.00 0.00 37.74 2.52
398 890 1.952296 CAGATGCTATGGCCCAGAAAC 59.048 52.381 0.00 0.00 37.74 2.78
399 891 1.849039 AGATGCTATGGCCCAGAAACT 59.151 47.619 0.00 0.00 37.74 2.66
400 892 1.952296 GATGCTATGGCCCAGAAACTG 59.048 52.381 0.00 0.00 37.74 3.16
416 908 8.511604 CCAGAAACTGGTAATCTATGATTTGT 57.488 34.615 9.36 0.00 45.82 2.83
417 909 8.616076 CCAGAAACTGGTAATCTATGATTTGTC 58.384 37.037 9.36 0.00 45.82 3.18
418 910 9.388506 CAGAAACTGGTAATCTATGATTTGTCT 57.611 33.333 0.00 0.00 0.00 3.41
419 911 9.606631 AGAAACTGGTAATCTATGATTTGTCTC 57.393 33.333 0.00 0.00 0.00 3.36
420 912 9.606631 GAAACTGGTAATCTATGATTTGTCTCT 57.393 33.333 0.00 0.00 0.00 3.10
425 917 9.914131 TGGTAATCTATGATTTGTCTCTAATCG 57.086 33.333 0.00 0.00 35.29 3.34
426 918 9.915629 GGTAATCTATGATTTGTCTCTAATCGT 57.084 33.333 0.00 0.00 35.29 3.73
429 921 9.915629 AATCTATGATTTGTCTCTAATCGTACC 57.084 33.333 0.00 0.00 35.29 3.34
430 922 7.582352 TCTATGATTTGTCTCTAATCGTACCG 58.418 38.462 0.00 0.00 35.29 4.02
431 923 5.823209 TGATTTGTCTCTAATCGTACCGA 57.177 39.130 0.00 0.00 41.13 4.69
432 924 5.817988 TGATTTGTCTCTAATCGTACCGAG 58.182 41.667 0.00 0.00 39.91 4.63
433 925 5.356190 TGATTTGTCTCTAATCGTACCGAGT 59.644 40.000 0.00 0.00 39.91 4.18
434 926 4.611310 TTGTCTCTAATCGTACCGAGTG 57.389 45.455 0.00 0.00 39.91 3.51
435 927 3.603532 TGTCTCTAATCGTACCGAGTGT 58.396 45.455 0.00 0.00 39.91 3.55
436 928 4.005650 TGTCTCTAATCGTACCGAGTGTT 58.994 43.478 0.00 0.00 39.91 3.32
437 929 4.142752 TGTCTCTAATCGTACCGAGTGTTG 60.143 45.833 0.00 0.00 39.91 3.33
438 930 3.376234 TCTCTAATCGTACCGAGTGTTGG 59.624 47.826 0.00 0.00 39.91 3.77
439 931 3.346315 TCTAATCGTACCGAGTGTTGGA 58.654 45.455 0.00 0.00 39.91 3.53
440 932 2.358939 AATCGTACCGAGTGTTGGAC 57.641 50.000 0.00 0.00 39.91 4.02
441 933 0.169672 ATCGTACCGAGTGTTGGACG 59.830 55.000 0.00 0.00 39.91 4.79
448 940 2.875080 CGAGTGTTGGACGGAAATTC 57.125 50.000 0.00 0.00 0.00 2.17
449 941 2.139917 CGAGTGTTGGACGGAAATTCA 58.860 47.619 0.00 0.00 0.00 2.57
450 942 2.742053 CGAGTGTTGGACGGAAATTCAT 59.258 45.455 0.00 0.00 0.00 2.57
451 943 3.181520 CGAGTGTTGGACGGAAATTCATC 60.182 47.826 0.00 0.00 0.00 2.92
452 944 2.742053 AGTGTTGGACGGAAATTCATCG 59.258 45.455 0.00 0.00 0.00 3.84
453 945 2.482721 GTGTTGGACGGAAATTCATCGT 59.517 45.455 0.00 0.00 39.99 3.73
454 946 3.680937 GTGTTGGACGGAAATTCATCGTA 59.319 43.478 0.00 0.00 37.25 3.43
455 947 3.680937 TGTTGGACGGAAATTCATCGTAC 59.319 43.478 0.96 0.96 37.25 3.67
456 948 2.532235 TGGACGGAAATTCATCGTACG 58.468 47.619 9.53 9.53 40.29 3.67
457 949 2.094597 TGGACGGAAATTCATCGTACGT 60.095 45.455 16.05 0.00 40.29 3.57
458 950 3.128415 TGGACGGAAATTCATCGTACGTA 59.872 43.478 16.05 2.34 40.29 3.57
459 951 4.202040 TGGACGGAAATTCATCGTACGTAT 60.202 41.667 16.05 4.80 40.29 3.06
460 952 5.008514 TGGACGGAAATTCATCGTACGTATA 59.991 40.000 16.05 0.00 40.29 1.47
461 953 5.566774 GGACGGAAATTCATCGTACGTATAG 59.433 44.000 16.05 4.06 37.25 1.31
462 954 4.913924 ACGGAAATTCATCGTACGTATAGC 59.086 41.667 16.05 0.00 35.23 2.97
463 955 4.913345 CGGAAATTCATCGTACGTATAGCA 59.087 41.667 16.05 0.00 0.00 3.49
464 956 5.400188 CGGAAATTCATCGTACGTATAGCAA 59.600 40.000 16.05 1.63 0.00 3.91
465 957 6.398621 CGGAAATTCATCGTACGTATAGCAAG 60.399 42.308 16.05 0.00 0.00 4.01
466 958 6.128902 GGAAATTCATCGTACGTATAGCAAGG 60.129 42.308 16.05 0.00 0.00 3.61
467 959 4.906065 TTCATCGTACGTATAGCAAGGT 57.094 40.909 16.05 0.00 0.00 3.50
468 960 4.906065 TCATCGTACGTATAGCAAGGTT 57.094 40.909 16.05 0.00 0.00 3.50
469 961 4.852138 TCATCGTACGTATAGCAAGGTTC 58.148 43.478 16.05 0.00 0.00 3.62
490 982 6.183360 GGTTCTATGACAATATTGCTTGTGCT 60.183 38.462 15.48 0.00 39.40 4.40
549 1041 2.803386 TGCTTGTGCTTGATTGCAATTG 59.197 40.909 14.33 8.35 45.12 2.32
559 1051 5.402997 TTGATTGCAATTGTCCATGCTAA 57.597 34.783 14.33 0.00 42.97 3.09
563 1055 6.879993 TGATTGCAATTGTCCATGCTAAAAAT 59.120 30.769 14.33 0.00 42.97 1.82
566 1058 8.789825 TTGCAATTGTCCATGCTAAAAATTAT 57.210 26.923 7.40 0.00 42.97 1.28
629 1122 5.576563 TCAGAGGTTCCAAAAGTATTGGA 57.423 39.130 5.83 5.83 46.08 3.53
646 1139 0.833949 GGAGGAAAGGACCTAGCTGG 59.166 60.000 0.00 0.00 40.73 4.85
665 1158 2.758979 TGGACCAAGAGGAGTCGATTAC 59.241 50.000 0.00 0.00 38.69 1.89
667 1160 3.181485 GGACCAAGAGGAGTCGATTACTG 60.181 52.174 0.00 0.00 39.07 2.74
687 1180 1.800805 CATGGACTATGGCGGACATC 58.199 55.000 0.00 0.00 41.03 3.06
709 1202 6.048732 TCACAATGTTGAGCCAGAATAGTA 57.951 37.500 0.00 0.00 0.00 1.82
747 1240 1.478510 CTGGTCGAGTAGAAGCACCAT 59.521 52.381 0.00 0.00 36.54 3.55
772 1265 4.405116 ACAGTTTAGGTCACGTTGGTTA 57.595 40.909 0.00 0.00 0.00 2.85
815 1312 9.830975 AAATAAAGTAAGCAAACAATTGGAACT 57.169 25.926 10.83 0.00 37.02 3.01
830 1328 2.087646 GGAACTGATGAGTTGCCCTTC 58.912 52.381 1.00 0.00 43.02 3.46
912 1410 5.473273 TCTCCTTCCTGCCCTATAAATACA 58.527 41.667 0.00 0.00 0.00 2.29
954 1452 4.442073 CGCATCACCTTTTCAAAGTCTTTG 59.558 41.667 17.73 17.73 41.96 2.77
981 1479 3.692101 AGTGACATAGTCTTCTGGAGTCG 59.308 47.826 0.00 0.00 33.15 4.18
996 1494 1.000618 GAGTCGGGGAAAAAGTCGAGT 59.999 52.381 0.00 0.00 37.90 4.18
1019 1517 2.882761 CCATGATCGCTGAAATGGATGT 59.117 45.455 13.50 0.00 41.84 3.06
1112 1610 3.181497 GGTATGTGTTCATGCATGTCACC 60.181 47.826 32.36 24.06 38.19 4.02
1323 1828 9.840427 CAAACTGAGGTGAAATATATTCGTTTT 57.160 29.630 0.00 0.00 0.00 2.43
1346 1851 4.649674 TCAGCCGTTCTCCTATAGAATTGT 59.350 41.667 0.00 0.00 45.84 2.71
1441 1988 1.203001 TCTTGGGCCTTGTTCGGATTT 60.203 47.619 4.53 0.00 0.00 2.17
1480 2027 3.136626 GCTCCCCACCAGTATATTGTTCT 59.863 47.826 0.00 0.00 0.00 3.01
1486 2033 6.542370 CCCCACCAGTATATTGTTCTAACTTG 59.458 42.308 0.00 0.00 0.00 3.16
1611 2175 1.153568 CTCTTTCGGATGGCGCTCA 60.154 57.895 7.64 3.81 0.00 4.26
1619 2183 0.101219 GGATGGCGCTCACCAATTTC 59.899 55.000 7.64 0.00 44.65 2.17
1621 2185 0.676466 ATGGCGCTCACCAATTTCGA 60.676 50.000 7.64 0.00 44.65 3.71
1817 2604 1.888512 CCATGCTGCAACCTAAACACT 59.111 47.619 6.36 0.00 0.00 3.55
2121 2937 4.403432 GGGTCATTTCCATGATGTCAACAT 59.597 41.667 0.00 0.00 41.64 2.71
2260 3076 8.779354 ATGTCTTTTAAGAATGTGAGTAGTCC 57.221 34.615 0.00 0.00 36.68 3.85
2263 3079 9.220767 GTCTTTTAAGAATGTGAGTAGTCCAAT 57.779 33.333 0.00 0.00 36.68 3.16
2264 3080 9.793259 TCTTTTAAGAATGTGAGTAGTCCAATT 57.207 29.630 0.00 0.00 30.73 2.32
2329 3145 5.237127 GCTTTTCCATTCAAAACCTTTCAGG 59.763 40.000 0.00 0.00 42.49 3.86
2450 3266 3.304861 GGGTTTAGCCAAGGTTTTACACG 60.305 47.826 0.00 0.00 39.65 4.49
2496 3312 4.371855 TGTTCCACTCGTAGCTGATAAG 57.628 45.455 0.00 0.00 0.00 1.73
2503 3319 3.570550 ACTCGTAGCTGATAAGTGGGATC 59.429 47.826 0.00 0.00 0.00 3.36
2542 3358 3.355378 TCATTGGCCATTGAAGTAGTGG 58.645 45.455 24.51 0.00 39.09 4.00
2559 3375 0.911769 TGGTCCTCCCTTATGCACAG 59.088 55.000 0.00 0.00 0.00 3.66
2595 3411 2.711542 AGTTAAGGGCATGTCCTTTCG 58.288 47.619 35.18 0.00 44.14 3.46
2606 3422 5.449999 GGCATGTCCTTTCGGGTATTAAAAG 60.450 44.000 0.00 0.00 36.25 2.27
2616 3432 8.898983 TTTCGGGTATTAAAAGATTAAAAGCG 57.101 30.769 0.00 0.00 34.80 4.68
2739 3960 5.049167 TGTGTTGAAAGAAAATCATGGTGC 58.951 37.500 0.00 0.00 0.00 5.01
2778 3999 9.533253 TTTCATTGAAGAAAAGATTTGTCCTTC 57.467 29.630 0.00 0.00 34.77 3.46
2910 4131 8.755696 TTTGAAAGGTATGATGTGTTTATTGC 57.244 30.769 0.00 0.00 0.00 3.56
3149 4370 3.062099 GTGTACATCATCGTCGTTTGCAT 59.938 43.478 0.00 0.00 0.00 3.96
3180 4401 8.227119 CCATTAATCCGAAAACAATTTGGAAAC 58.773 33.333 0.78 0.00 32.91 2.78
3200 4421 4.471904 ACTGAGTGCCGAATCAATTAGA 57.528 40.909 0.00 0.00 0.00 2.10
3245 4466 8.622948 ATTAGTTAGCCAGCCAGTTAATTATC 57.377 34.615 0.00 0.00 0.00 1.75
3313 4535 5.163353 ACGGAATCAATTTGGAAACCAAGTT 60.163 36.000 5.64 5.64 44.84 2.66
3324 4546 8.964476 TTTGGAAACCAAGTTATTAATGCAAA 57.036 26.923 0.00 0.00 44.84 3.68
3413 4635 4.138487 AGTTTTCCTAATAGTCTGCCCG 57.862 45.455 0.00 0.00 0.00 6.13
3461 4683 7.042051 TCCAAAACTTCATATAATCTAGCACGC 60.042 37.037 0.00 0.00 0.00 5.34
3476 4698 1.148273 ACGCCACATGTCACCACTT 59.852 52.632 0.00 0.00 0.00 3.16
3496 4718 8.650490 ACCACTTTTCAAATATTGTTTCATCCT 58.350 29.630 0.00 0.00 0.00 3.24
3522 4744 1.787012 GCATGCCACCACTTTTCAAG 58.213 50.000 6.36 0.00 0.00 3.02
3532 4754 3.701040 ACCACTTTTCAAGAGCACATGTT 59.299 39.130 0.00 0.00 0.00 2.71
3595 4818 6.759497 AAGACTTGCTTGTGAACTAAAAGT 57.241 33.333 0.00 0.00 34.93 2.66
3599 4822 6.092748 ACTTGCTTGTGAACTAAAAGTTGTG 58.907 36.000 0.00 0.00 38.80 3.33
3999 5260 5.119694 CCAAGAGAGAACTAATAGCCAACC 58.880 45.833 0.00 0.00 0.00 3.77
4147 5446 8.856153 ATACATTTGTTACATGTGGACAACTA 57.144 30.769 21.85 13.23 35.57 2.24
4725 6087 0.833287 CCATCCTCACAGATTCGGGT 59.167 55.000 0.00 0.00 0.00 5.28
5465 6871 3.596214 ACTAAACCAGCGACAGGTAATG 58.404 45.455 0.00 0.00 38.76 1.90
5787 7196 1.135915 AGACCTCACTGTCGCATCATC 59.864 52.381 0.00 0.00 40.26 2.92
5788 7197 0.179127 ACCTCACTGTCGCATCATCG 60.179 55.000 0.00 0.00 0.00 3.84
5825 7234 5.241662 GGAGACAAAGATGTGCTTTCTAGT 58.758 41.667 0.00 0.00 44.83 2.57
5828 7237 7.148557 GGAGACAAAGATGTGCTTTCTAGTAAC 60.149 40.741 0.00 0.00 44.83 2.50
5829 7238 7.217200 AGACAAAGATGTGCTTTCTAGTAACA 58.783 34.615 0.00 0.00 44.83 2.41
5832 7241 7.499232 ACAAAGATGTGCTTTCTAGTAACAAGT 59.501 33.333 0.00 0.00 44.83 3.16
5833 7242 8.345565 CAAAGATGTGCTTTCTAGTAACAAGTT 58.654 33.333 0.00 0.00 44.83 2.66
5834 7243 8.451908 AAGATGTGCTTTCTAGTAACAAGTTT 57.548 30.769 0.00 0.00 31.11 2.66
5835 7244 8.089115 AGATGTGCTTTCTAGTAACAAGTTTC 57.911 34.615 0.00 0.00 0.00 2.78
5836 7245 6.613755 TGTGCTTTCTAGTAACAAGTTTCC 57.386 37.500 0.00 0.00 0.00 3.13
5837 7246 6.116806 TGTGCTTTCTAGTAACAAGTTTCCA 58.883 36.000 0.00 0.00 0.00 3.53
5838 7247 6.260050 TGTGCTTTCTAGTAACAAGTTTCCAG 59.740 38.462 0.00 0.00 0.00 3.86
5839 7248 6.482308 GTGCTTTCTAGTAACAAGTTTCCAGA 59.518 38.462 0.00 0.00 0.00 3.86
5840 7249 6.482308 TGCTTTCTAGTAACAAGTTTCCAGAC 59.518 38.462 0.00 0.00 0.00 3.51
5841 7250 6.706716 GCTTTCTAGTAACAAGTTTCCAGACT 59.293 38.462 0.00 0.00 0.00 3.24
5842 7251 7.307455 GCTTTCTAGTAACAAGTTTCCAGACTG 60.307 40.741 0.00 0.00 0.00 3.51
5843 7252 6.971726 TCTAGTAACAAGTTTCCAGACTGA 57.028 37.500 3.32 0.00 0.00 3.41
5844 7253 7.356089 TCTAGTAACAAGTTTCCAGACTGAA 57.644 36.000 3.32 0.00 0.00 3.02
5845 7254 7.788026 TCTAGTAACAAGTTTCCAGACTGAAA 58.212 34.615 3.32 0.20 32.02 2.69
5846 7255 8.262227 TCTAGTAACAAGTTTCCAGACTGAAAA 58.738 33.333 3.32 0.00 36.09 2.29
5847 7256 7.696992 AGTAACAAGTTTCCAGACTGAAAAA 57.303 32.000 3.32 1.55 36.09 1.94
5883 7292 1.225855 CCAGCAGTACAACGCTTTGA 58.774 50.000 10.27 0.00 35.96 2.69
5914 7323 7.822658 AGTAGAACTGTAGAAGTGACTGATTC 58.177 38.462 0.00 0.00 39.81 2.52
5966 7375 0.309922 CTCACCTGTTGTTGCTGCTG 59.690 55.000 0.00 0.00 0.00 4.41
5999 7408 0.666913 GTGATGCCACCATGATCAGC 59.333 55.000 0.09 0.00 37.33 4.26
6000 7409 0.816421 TGATGCCACCATGATCAGCG 60.816 55.000 0.09 0.00 0.00 5.18
6001 7410 1.512996 GATGCCACCATGATCAGCGG 61.513 60.000 11.53 11.53 0.00 5.52
6002 7411 2.903855 GCCACCATGATCAGCGGG 60.904 66.667 16.26 12.60 0.00 6.13
6003 7412 2.203252 CCACCATGATCAGCGGGG 60.203 66.667 16.26 12.79 0.00 5.73
6004 7413 2.203252 CACCATGATCAGCGGGGG 60.203 66.667 16.26 8.47 0.00 5.40
6005 7414 2.692368 ACCATGATCAGCGGGGGT 60.692 61.111 16.26 8.84 0.00 4.95
6006 7415 2.203252 CCATGATCAGCGGGGGTG 60.203 66.667 0.09 0.00 0.00 4.61
6007 7416 2.745308 CCATGATCAGCGGGGGTGA 61.745 63.158 0.09 0.00 44.17 4.02
6011 7420 4.195334 ATCAGCGGGGGTGATGCC 62.195 66.667 9.29 0.00 46.87 4.40
6034 7443 3.090790 CCATGATCAACATCACCAACCA 58.909 45.455 0.00 0.00 42.05 3.67
6049 7458 2.591429 CCATGCGCGCATTCCCTA 60.591 61.111 41.73 16.42 33.90 3.53
6060 7469 3.732212 CGCATTCCCTATCAATCTGTCA 58.268 45.455 0.00 0.00 0.00 3.58
6080 7489 0.824109 CTCGCCTAGACCATTGACCA 59.176 55.000 0.00 0.00 0.00 4.02
6117 7526 5.045651 TGACTATGACCATGACCATTGACTT 60.046 40.000 12.66 0.00 0.00 3.01
6118 7527 5.819991 ACTATGACCATGACCATTGACTTT 58.180 37.500 12.66 0.00 0.00 2.66
6119 7528 5.649395 ACTATGACCATGACCATTGACTTTG 59.351 40.000 12.66 0.00 0.00 2.77
6130 7539 7.257722 TGACCATTGACTTTGAAAAGAAGTTC 58.742 34.615 9.71 0.00 37.46 3.01
6214 7623 6.583806 AGATTTGCAAAATGTTCACGAGATTC 59.416 34.615 17.19 3.82 0.00 2.52
6405 7814 4.426313 GGAGGTTCGGGGGCCTTG 62.426 72.222 0.84 0.00 34.81 3.61
6406 7815 3.327404 GAGGTTCGGGGGCCTTGA 61.327 66.667 0.84 0.00 34.81 3.02
6407 7816 3.623703 GAGGTTCGGGGGCCTTGAC 62.624 68.421 0.84 0.00 34.81 3.18
6408 7817 3.961414 GGTTCGGGGGCCTTGACA 61.961 66.667 0.84 0.00 0.00 3.58
6409 7818 2.359975 GTTCGGGGGCCTTGACAG 60.360 66.667 0.84 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.713826 TTAAAATCGGAGAAGGCCAGT 57.286 42.857 5.01 0.00 43.58 4.00
10 11 4.734695 GCAATTAAAATCGGAGAAGGCCAG 60.735 45.833 5.01 0.00 43.58 4.85
21 22 6.033831 GTGTTCCTGACATGCAATTAAAATCG 59.966 38.462 0.00 0.00 41.10 3.34
35 36 2.398588 ACTTCCAGAGTGTTCCTGACA 58.601 47.619 0.00 0.00 37.17 3.58
49 50 3.496160 GGCTTCTGGAGTGTTAACTTCCA 60.496 47.826 22.68 22.68 36.52 3.53
50 51 3.075148 GGCTTCTGGAGTGTTAACTTCC 58.925 50.000 17.66 17.66 36.52 3.46
51 52 3.740115 TGGCTTCTGGAGTGTTAACTTC 58.260 45.455 7.22 4.80 36.52 3.01
52 53 3.744660 CTGGCTTCTGGAGTGTTAACTT 58.255 45.455 7.22 0.00 36.52 2.66
53 54 2.551071 GCTGGCTTCTGGAGTGTTAACT 60.551 50.000 7.22 0.00 40.21 2.24
54 55 1.807142 GCTGGCTTCTGGAGTGTTAAC 59.193 52.381 0.00 0.00 0.00 2.01
55 56 1.419762 TGCTGGCTTCTGGAGTGTTAA 59.580 47.619 0.00 0.00 0.00 2.01
56 57 1.002430 CTGCTGGCTTCTGGAGTGTTA 59.998 52.381 0.00 0.00 0.00 2.41
92 93 6.652053 TGGTTAACCAACAACTAGTAGTGTT 58.348 36.000 25.19 7.06 44.35 3.32
93 94 6.237887 TGGTTAACCAACAACTAGTAGTGT 57.762 37.500 25.19 0.00 44.35 3.55
135 627 6.176014 ACATGGTTCCTATTTAGTCCTAGC 57.824 41.667 0.00 0.00 0.00 3.42
144 636 5.104067 GGAAGAGGGTACATGGTTCCTATTT 60.104 44.000 10.28 5.94 31.83 1.40
146 638 3.974642 GGAAGAGGGTACATGGTTCCTAT 59.025 47.826 0.00 0.00 32.33 2.57
179 671 9.915629 AGTTGAGACTAATAAATGGATATCGTC 57.084 33.333 0.00 0.00 33.32 4.20
180 672 9.698309 CAGTTGAGACTAATAAATGGATATCGT 57.302 33.333 0.00 0.00 33.90 3.73
181 673 9.144747 CCAGTTGAGACTAATAAATGGATATCG 57.855 37.037 7.07 0.00 40.83 2.92
220 712 7.553044 AGAAACCATTCGGATTCCTAAAAGTAG 59.447 37.037 0.30 0.00 43.41 2.57
267 759 9.737427 CGAGTCTATTGTTTCAGTCATAGTTAT 57.263 33.333 0.00 0.00 0.00 1.89
268 760 8.737175 ACGAGTCTATTGTTTCAGTCATAGTTA 58.263 33.333 0.00 0.00 0.00 2.24
269 761 7.603651 ACGAGTCTATTGTTTCAGTCATAGTT 58.396 34.615 0.00 0.00 0.00 2.24
270 762 7.159322 ACGAGTCTATTGTTTCAGTCATAGT 57.841 36.000 0.00 0.00 0.00 2.12
271 763 7.971168 AGAACGAGTCTATTGTTTCAGTCATAG 59.029 37.037 0.00 0.00 35.52 2.23
272 764 7.827701 AGAACGAGTCTATTGTTTCAGTCATA 58.172 34.615 0.00 0.00 35.52 2.15
273 765 6.692486 AGAACGAGTCTATTGTTTCAGTCAT 58.308 36.000 0.00 0.00 35.52 3.06
274 766 6.085555 AGAACGAGTCTATTGTTTCAGTCA 57.914 37.500 0.00 0.00 35.52 3.41
275 767 6.089685 GGAAGAACGAGTCTATTGTTTCAGTC 59.910 42.308 0.00 0.00 35.52 3.51
276 768 5.927115 GGAAGAACGAGTCTATTGTTTCAGT 59.073 40.000 0.00 0.00 35.52 3.41
277 769 6.159988 AGGAAGAACGAGTCTATTGTTTCAG 58.840 40.000 0.00 0.00 35.52 3.02
278 770 6.097915 AGGAAGAACGAGTCTATTGTTTCA 57.902 37.500 0.00 0.00 35.52 2.69
279 771 8.705048 AATAGGAAGAACGAGTCTATTGTTTC 57.295 34.615 0.00 0.00 35.52 2.78
280 772 7.764901 GGAATAGGAAGAACGAGTCTATTGTTT 59.235 37.037 0.00 0.00 35.52 2.83
281 773 7.266400 GGAATAGGAAGAACGAGTCTATTGTT 58.734 38.462 0.00 0.00 38.29 2.83
282 774 6.183360 GGGAATAGGAAGAACGAGTCTATTGT 60.183 42.308 0.00 0.00 34.56 2.71
283 775 6.217294 GGGAATAGGAAGAACGAGTCTATTG 58.783 44.000 0.00 0.00 34.56 1.90
284 776 5.009811 CGGGAATAGGAAGAACGAGTCTATT 59.990 44.000 0.00 0.00 34.56 1.73
285 777 4.519730 CGGGAATAGGAAGAACGAGTCTAT 59.480 45.833 0.00 0.00 34.56 1.98
286 778 3.881688 CGGGAATAGGAAGAACGAGTCTA 59.118 47.826 0.00 0.00 34.56 2.59
287 779 2.688958 CGGGAATAGGAAGAACGAGTCT 59.311 50.000 0.00 0.00 38.69 3.24
292 784 1.409427 AGCTCGGGAATAGGAAGAACG 59.591 52.381 0.00 0.00 0.00 3.95
308 800 3.812053 AGTTTCGATTGCCATATCAGCTC 59.188 43.478 0.00 0.00 0.00 4.09
310 802 3.851105 GCAGTTTCGATTGCCATATCAGC 60.851 47.826 5.95 0.00 34.28 4.26
311 803 3.562973 AGCAGTTTCGATTGCCATATCAG 59.437 43.478 11.89 0.00 41.17 2.90
312 804 3.544684 AGCAGTTTCGATTGCCATATCA 58.455 40.909 11.89 0.00 41.17 2.15
313 805 3.812053 AGAGCAGTTTCGATTGCCATATC 59.188 43.478 11.89 5.22 41.17 1.63
314 806 3.813443 AGAGCAGTTTCGATTGCCATAT 58.187 40.909 11.89 0.00 41.17 1.78
315 807 3.266510 AGAGCAGTTTCGATTGCCATA 57.733 42.857 11.89 0.00 41.17 2.74
316 808 2.119801 AGAGCAGTTTCGATTGCCAT 57.880 45.000 11.89 1.22 41.17 4.40
317 809 2.346803 GTAGAGCAGTTTCGATTGCCA 58.653 47.619 11.89 0.00 41.17 4.92
318 810 1.324736 CGTAGAGCAGTTTCGATTGCC 59.675 52.381 11.89 5.78 41.17 4.52
319 811 1.993370 ACGTAGAGCAGTTTCGATTGC 59.007 47.619 8.52 8.52 40.57 3.56
320 812 3.237660 CGTACGTAGAGCAGTTTCGATTG 59.762 47.826 7.22 0.00 0.00 2.67
321 813 3.125829 TCGTACGTAGAGCAGTTTCGATT 59.874 43.478 16.05 0.00 0.00 3.34
322 814 2.674852 TCGTACGTAGAGCAGTTTCGAT 59.325 45.455 16.05 0.00 0.00 3.59
323 815 2.068519 TCGTACGTAGAGCAGTTTCGA 58.931 47.619 16.05 0.00 0.00 3.71
324 816 2.515641 TCGTACGTAGAGCAGTTTCG 57.484 50.000 16.05 0.00 0.00 3.46
325 817 4.660105 AGAATCGTACGTAGAGCAGTTTC 58.340 43.478 16.05 6.01 0.00 2.78
326 818 4.698583 AGAATCGTACGTAGAGCAGTTT 57.301 40.909 16.05 0.00 0.00 2.66
327 819 4.698583 AAGAATCGTACGTAGAGCAGTT 57.301 40.909 16.05 0.00 0.00 3.16
328 820 4.698583 AAAGAATCGTACGTAGAGCAGT 57.301 40.909 16.05 0.00 0.00 4.40
348 840 2.094803 TCGTACCAGCGTCCGATAAAAA 60.095 45.455 0.00 0.00 0.00 1.94
349 841 1.472082 TCGTACCAGCGTCCGATAAAA 59.528 47.619 0.00 0.00 0.00 1.52
350 842 1.093972 TCGTACCAGCGTCCGATAAA 58.906 50.000 0.00 0.00 0.00 1.40
351 843 0.378257 GTCGTACCAGCGTCCGATAA 59.622 55.000 0.00 0.00 32.63 1.75
352 844 1.439353 GGTCGTACCAGCGTCCGATA 61.439 60.000 0.00 0.00 38.42 2.92
353 845 2.768492 GGTCGTACCAGCGTCCGAT 61.768 63.158 0.00 0.00 38.42 4.18
354 846 3.434319 GGTCGTACCAGCGTCCGA 61.434 66.667 0.00 0.00 38.42 4.55
355 847 3.740397 TGGTCGTACCAGCGTCCG 61.740 66.667 3.02 0.00 44.79 4.79
363 855 2.607187 CATCTGTTGTCTGGTCGTACC 58.393 52.381 0.00 0.00 39.22 3.34
364 856 1.993370 GCATCTGTTGTCTGGTCGTAC 59.007 52.381 0.00 0.00 0.00 3.67
365 857 1.893137 AGCATCTGTTGTCTGGTCGTA 59.107 47.619 0.00 0.00 0.00 3.43
366 858 0.681733 AGCATCTGTTGTCTGGTCGT 59.318 50.000 0.00 0.00 0.00 4.34
367 859 2.654749 TAGCATCTGTTGTCTGGTCG 57.345 50.000 0.00 0.00 0.00 4.79
368 860 3.201290 CCATAGCATCTGTTGTCTGGTC 58.799 50.000 0.00 0.00 0.00 4.02
369 861 2.681976 GCCATAGCATCTGTTGTCTGGT 60.682 50.000 0.00 0.00 39.53 4.00
370 862 1.945394 GCCATAGCATCTGTTGTCTGG 59.055 52.381 0.00 0.00 39.53 3.86
371 863 1.945394 GGCCATAGCATCTGTTGTCTG 59.055 52.381 0.00 0.00 42.56 3.51
372 864 1.133976 GGGCCATAGCATCTGTTGTCT 60.134 52.381 4.39 0.00 42.56 3.41
373 865 1.312815 GGGCCATAGCATCTGTTGTC 58.687 55.000 4.39 0.00 42.56 3.18
374 866 0.625316 TGGGCCATAGCATCTGTTGT 59.375 50.000 0.00 0.00 42.56 3.32
375 867 1.134007 TCTGGGCCATAGCATCTGTTG 60.134 52.381 6.72 0.00 42.56 3.33
376 868 1.216064 TCTGGGCCATAGCATCTGTT 58.784 50.000 6.72 0.00 42.56 3.16
377 869 1.216064 TTCTGGGCCATAGCATCTGT 58.784 50.000 6.72 0.00 42.56 3.41
378 870 1.952296 GTTTCTGGGCCATAGCATCTG 59.048 52.381 6.72 0.00 42.56 2.90
379 871 1.849039 AGTTTCTGGGCCATAGCATCT 59.151 47.619 6.72 0.00 42.56 2.90
380 872 1.952296 CAGTTTCTGGGCCATAGCATC 59.048 52.381 6.72 0.00 42.56 3.91
381 873 2.062971 CAGTTTCTGGGCCATAGCAT 57.937 50.000 6.72 0.00 42.56 3.79
382 874 3.575506 CAGTTTCTGGGCCATAGCA 57.424 52.632 6.72 0.00 42.56 3.49
392 884 9.388506 AGACAAATCATAGATTACCAGTTTCTG 57.611 33.333 0.00 0.00 0.00 3.02
393 885 9.606631 GAGACAAATCATAGATTACCAGTTTCT 57.393 33.333 0.00 0.00 0.00 2.52
394 886 9.606631 AGAGACAAATCATAGATTACCAGTTTC 57.393 33.333 0.00 0.00 0.00 2.78
399 891 9.914131 CGATTAGAGACAAATCATAGATTACCA 57.086 33.333 0.00 0.00 33.75 3.25
400 892 9.915629 ACGATTAGAGACAAATCATAGATTACC 57.084 33.333 0.00 0.00 33.75 2.85
403 895 9.915629 GGTACGATTAGAGACAAATCATAGATT 57.084 33.333 0.00 0.00 33.75 2.40
425 917 0.314935 TTCCGTCCAACACTCGGTAC 59.685 55.000 0.00 0.00 43.94 3.34
426 918 1.039068 TTTCCGTCCAACACTCGGTA 58.961 50.000 0.00 0.00 43.94 4.02
427 919 0.395312 ATTTCCGTCCAACACTCGGT 59.605 50.000 0.00 0.00 43.94 4.69
428 920 1.463444 GAATTTCCGTCCAACACTCGG 59.537 52.381 0.00 0.00 44.76 4.63
429 921 2.139917 TGAATTTCCGTCCAACACTCG 58.860 47.619 0.00 0.00 0.00 4.18
430 922 3.181520 CGATGAATTTCCGTCCAACACTC 60.182 47.826 0.00 0.00 0.00 3.51
431 923 2.742053 CGATGAATTTCCGTCCAACACT 59.258 45.455 0.00 0.00 0.00 3.55
432 924 2.482721 ACGATGAATTTCCGTCCAACAC 59.517 45.455 0.00 0.00 29.82 3.32
433 925 2.773487 ACGATGAATTTCCGTCCAACA 58.227 42.857 0.00 0.00 29.82 3.33
434 926 3.241868 CGTACGATGAATTTCCGTCCAAC 60.242 47.826 10.44 0.00 37.69 3.77
435 927 2.924926 CGTACGATGAATTTCCGTCCAA 59.075 45.455 10.44 0.00 37.69 3.53
436 928 2.094597 ACGTACGATGAATTTCCGTCCA 60.095 45.455 24.41 0.00 37.69 4.02
437 929 2.533266 ACGTACGATGAATTTCCGTCC 58.467 47.619 24.41 0.00 37.69 4.79
438 930 5.058977 GCTATACGTACGATGAATTTCCGTC 59.941 44.000 24.41 0.00 37.69 4.79
439 931 4.913924 GCTATACGTACGATGAATTTCCGT 59.086 41.667 24.41 6.09 39.94 4.69
440 932 4.913345 TGCTATACGTACGATGAATTTCCG 59.087 41.667 24.41 0.07 0.00 4.30
441 933 6.128902 CCTTGCTATACGTACGATGAATTTCC 60.129 42.308 24.41 1.57 0.00 3.13
442 934 6.420008 ACCTTGCTATACGTACGATGAATTTC 59.580 38.462 24.41 3.67 0.00 2.17
443 935 6.278363 ACCTTGCTATACGTACGATGAATTT 58.722 36.000 24.41 0.00 0.00 1.82
444 936 5.839621 ACCTTGCTATACGTACGATGAATT 58.160 37.500 24.41 0.00 0.00 2.17
445 937 5.449107 ACCTTGCTATACGTACGATGAAT 57.551 39.130 24.41 11.69 0.00 2.57
446 938 4.906065 ACCTTGCTATACGTACGATGAA 57.094 40.909 24.41 4.52 0.00 2.57
447 939 4.577693 AGAACCTTGCTATACGTACGATGA 59.422 41.667 24.41 7.02 0.00 2.92
448 940 4.856664 AGAACCTTGCTATACGTACGATG 58.143 43.478 24.41 9.48 0.00 3.84
449 941 6.429078 TCATAGAACCTTGCTATACGTACGAT 59.571 38.462 24.41 13.27 0.00 3.73
450 942 5.759763 TCATAGAACCTTGCTATACGTACGA 59.240 40.000 24.41 6.04 0.00 3.43
451 943 5.850128 GTCATAGAACCTTGCTATACGTACG 59.150 44.000 15.01 15.01 0.00 3.67
452 944 6.732154 TGTCATAGAACCTTGCTATACGTAC 58.268 40.000 0.00 0.00 0.00 3.67
453 945 6.947644 TGTCATAGAACCTTGCTATACGTA 57.052 37.500 0.00 0.00 0.00 3.57
454 946 5.847111 TGTCATAGAACCTTGCTATACGT 57.153 39.130 0.00 0.00 0.00 3.57
455 947 8.988064 ATATTGTCATAGAACCTTGCTATACG 57.012 34.615 0.00 0.00 0.00 3.06
457 949 9.219603 GCAATATTGTCATAGAACCTTGCTATA 57.780 33.333 16.61 0.00 34.99 1.31
458 950 7.941238 AGCAATATTGTCATAGAACCTTGCTAT 59.059 33.333 16.61 0.00 43.41 2.97
459 951 7.282585 AGCAATATTGTCATAGAACCTTGCTA 58.717 34.615 16.61 0.00 43.41 3.49
460 952 6.125029 AGCAATATTGTCATAGAACCTTGCT 58.875 36.000 16.61 1.19 41.23 3.91
461 953 6.382869 AGCAATATTGTCATAGAACCTTGC 57.617 37.500 16.61 0.00 37.36 4.01
462 954 7.699391 CACAAGCAATATTGTCATAGAACCTTG 59.301 37.037 16.61 17.24 41.41 3.61
463 955 7.629222 GCACAAGCAATATTGTCATAGAACCTT 60.629 37.037 16.61 5.52 41.41 3.50
464 956 6.183360 GCACAAGCAATATTGTCATAGAACCT 60.183 38.462 16.61 0.00 41.41 3.50
465 957 5.973565 GCACAAGCAATATTGTCATAGAACC 59.026 40.000 16.61 0.00 41.41 3.62
466 958 6.789262 AGCACAAGCAATATTGTCATAGAAC 58.211 36.000 16.61 0.00 41.41 3.01
467 959 7.395190 AAGCACAAGCAATATTGTCATAGAA 57.605 32.000 16.61 0.00 41.41 2.10
468 960 7.395190 AAAGCACAAGCAATATTGTCATAGA 57.605 32.000 16.61 0.00 41.41 1.98
469 961 7.543172 ACAAAAGCACAAGCAATATTGTCATAG 59.457 33.333 16.61 6.22 41.41 2.23
526 1018 2.823924 TGCAATCAAGCACAAGCAAT 57.176 40.000 0.00 0.00 45.49 3.56
530 1022 3.430895 GGACAATTGCAATCAAGCACAAG 59.569 43.478 13.38 0.00 45.61 3.16
629 1122 1.574263 GTCCAGCTAGGTCCTTTCCT 58.426 55.000 0.00 0.00 41.20 3.36
646 1139 3.735514 GCAGTAATCGACTCCTCTTGGTC 60.736 52.174 0.00 0.00 35.64 4.02
654 1147 2.101582 AGTCCATGCAGTAATCGACTCC 59.898 50.000 0.00 0.00 35.64 3.85
665 1158 0.882042 GTCCGCCATAGTCCATGCAG 60.882 60.000 0.00 0.00 32.84 4.41
667 1160 0.250467 ATGTCCGCCATAGTCCATGC 60.250 55.000 0.00 0.00 32.84 4.06
671 1164 0.464036 TGTGATGTCCGCCATAGTCC 59.536 55.000 0.00 0.00 32.56 3.85
687 1180 5.877012 ACTACTATTCTGGCTCAACATTGTG 59.123 40.000 0.00 0.00 0.00 3.33
709 1202 8.349568 TCGACCAGTATATATTATGCTCAACT 57.650 34.615 0.00 0.00 0.00 3.16
747 1240 5.184711 ACCAACGTGACCTAAACTGTAAAA 58.815 37.500 0.00 0.00 0.00 1.52
792 1289 8.001881 TCAGTTCCAATTGTTTGCTTACTTTA 57.998 30.769 4.43 0.00 0.00 1.85
793 1290 6.872920 TCAGTTCCAATTGTTTGCTTACTTT 58.127 32.000 4.43 0.00 0.00 2.66
796 1293 6.446318 TCATCAGTTCCAATTGTTTGCTTAC 58.554 36.000 4.43 0.00 0.00 2.34
815 1312 2.553028 GGAACTGAAGGGCAACTCATCA 60.553 50.000 0.00 0.00 0.00 3.07
830 1328 5.602628 GGACCAGCTATAGTTTAGGAACTG 58.397 45.833 0.84 0.00 45.46 3.16
912 1410 2.884720 GCGGGACTACCTATCTGGCTAT 60.885 54.545 0.00 0.00 40.22 2.97
954 1452 4.220821 TCCAGAAGACTATGTCACTTGGTC 59.779 45.833 0.00 0.00 34.60 4.02
981 1479 2.845363 TGGTACTCGACTTTTTCCCC 57.155 50.000 0.00 0.00 0.00 4.81
996 1494 3.836365 TCCATTTCAGCGATCATGGTA 57.164 42.857 7.23 0.00 37.92 3.25
1019 1517 0.391130 GTATCCTGCAACGCTGTCCA 60.391 55.000 0.00 0.00 0.00 4.02
1441 1988 7.776500 GGTGGGGAGCAAACTAAAATTATACTA 59.224 37.037 0.00 0.00 0.00 1.82
1817 2604 1.678635 GTACATGCTGCTTGCCCCA 60.679 57.895 14.63 0.00 42.00 4.96
1878 2665 5.574815 AAACACACGCTTGAATTAATTGC 57.425 34.783 5.17 2.18 0.00 3.56
2121 2937 1.409064 CTCTACTCGCAAGCCCATACA 59.591 52.381 0.00 0.00 37.18 2.29
2266 3082 6.799827 TCAAAATCCTCTATCCCTCCAAAAA 58.200 36.000 0.00 0.00 0.00 1.94
2267 3083 6.401537 TCAAAATCCTCTATCCCTCCAAAA 57.598 37.500 0.00 0.00 0.00 2.44
2377 3193 3.008049 AGTTAATCTCTTGGCACGGTCTT 59.992 43.478 0.00 0.00 0.00 3.01
2416 3232 1.203287 GCTAAACCCCGTCGACTAGTT 59.797 52.381 14.70 11.02 0.00 2.24
2426 3242 1.334160 AAAACCTTGGCTAAACCCCG 58.666 50.000 0.00 0.00 37.83 5.73
2517 3333 5.359009 CACTACTTCAATGGCCAATGAGAAT 59.641 40.000 22.32 14.44 0.00 2.40
2542 3358 2.237392 AGAACTGTGCATAAGGGAGGAC 59.763 50.000 0.00 0.00 0.00 3.85
2559 3375 9.320352 TGCCCTTAACTTTTAATTTTTGAGAAC 57.680 29.630 0.00 0.00 0.00 3.01
2595 3411 6.474427 GGCACGCTTTTAATCTTTTAATACCC 59.526 38.462 0.00 0.00 0.00 3.69
2606 3422 4.986622 AGAATCTTGGCACGCTTTTAATC 58.013 39.130 0.00 0.00 0.00 1.75
2739 3960 7.320443 TCTTCAATGAAATTATCGAACCCTG 57.680 36.000 0.00 0.00 32.46 4.45
2778 3999 5.289595 TCTCTTTCATGATATTTCCGACCG 58.710 41.667 0.00 0.00 0.00 4.79
2910 4131 5.940470 AGGGAGTATGTAAAAACTCTGCAAG 59.060 40.000 2.82 0.00 41.53 4.01
3149 4370 2.822561 TGTTTTCGGATTAATGGCTGCA 59.177 40.909 0.50 0.00 0.00 4.41
3180 4401 5.352569 ACTTTCTAATTGATTCGGCACTCAG 59.647 40.000 0.00 0.00 0.00 3.35
3200 4421 7.614494 ACTAATTGCATTAATGGCTTGACTTT 58.386 30.769 17.02 1.55 0.00 2.66
3245 4466 6.889301 ATATGGACCTAATGAATTGTGCAG 57.111 37.500 0.00 0.00 32.54 4.41
3286 4507 2.627863 TTCCAAATTGATTCCGTGCG 57.372 45.000 0.00 0.00 0.00 5.34
3287 4508 2.993220 GGTTTCCAAATTGATTCCGTGC 59.007 45.455 0.00 0.00 0.00 5.34
3288 4509 4.250116 TGGTTTCCAAATTGATTCCGTG 57.750 40.909 0.00 0.00 0.00 4.94
3289 4510 4.343814 ACTTGGTTTCCAAATTGATTCCGT 59.656 37.500 0.00 0.00 43.44 4.69
3413 4635 5.354513 GGAAACAATAGCTAGAAAGTGGACC 59.645 44.000 0.00 0.00 0.00 4.46
3461 4683 4.383850 TTTGAAAAGTGGTGACATGTGG 57.616 40.909 1.15 0.00 46.14 4.17
3476 4698 6.213195 AGGCCAGGATGAAACAATATTTGAAA 59.787 34.615 5.01 0.00 39.69 2.69
3522 4744 7.593825 AGGTGTAAATCTAAAAACATGTGCTC 58.406 34.615 0.00 0.00 0.00 4.26
3532 4754 9.743057 CACAATCAACAAGGTGTAAATCTAAAA 57.257 29.630 0.00 0.00 0.00 1.52
3999 5260 1.003545 CACAACCTTGTCAGTTGAGCG 60.004 52.381 10.38 0.00 46.03 5.03
4147 5446 3.003689 CCAAAGTGTCGTGCTCTTCATTT 59.996 43.478 0.00 0.00 31.31 2.32
4519 5832 7.923414 ATCACTTGGTACCTTAATCAAGTTC 57.077 36.000 14.36 0.00 44.88 3.01
4725 6087 1.241165 TGTCGAAGAAGTAGCGGTGA 58.759 50.000 0.00 0.00 39.69 4.02
5662 7071 1.068885 GTAGATCGGAGTCTCATGGCG 60.069 57.143 1.47 0.00 0.00 5.69
5787 7196 2.279451 TCCGATCCGCATGCTTCG 60.279 61.111 17.13 19.40 0.00 3.79
5788 7197 1.068083 TCTCCGATCCGCATGCTTC 59.932 57.895 17.13 8.94 0.00 3.86
5862 7271 2.139917 CAAAGCGTTGTACTGCTGGTA 58.860 47.619 4.01 0.00 41.46 3.25
5865 7274 3.542712 ATTCAAAGCGTTGTACTGCTG 57.457 42.857 12.18 0.00 41.46 4.41
5914 7323 0.733729 AGCCGCTACGACTCTACTTG 59.266 55.000 0.00 0.00 0.00 3.16
6004 7413 2.093890 TGTTGATCATGGTGGCATCAC 58.906 47.619 0.63 0.00 42.91 3.06
6005 7414 2.510928 TGTTGATCATGGTGGCATCA 57.489 45.000 1.35 1.35 0.00 3.07
6006 7415 2.953648 TGATGTTGATCATGGTGGCATC 59.046 45.455 0.00 5.33 36.83 3.91
6007 7416 2.691526 GTGATGTTGATCATGGTGGCAT 59.308 45.455 0.00 0.00 40.78 4.40
6008 7417 2.093890 GTGATGTTGATCATGGTGGCA 58.906 47.619 0.00 0.00 40.78 4.92
6009 7418 1.406539 GGTGATGTTGATCATGGTGGC 59.593 52.381 0.00 0.00 40.78 5.01
6010 7419 2.725637 TGGTGATGTTGATCATGGTGG 58.274 47.619 0.00 0.00 40.78 4.61
6011 7420 3.119388 GGTTGGTGATGTTGATCATGGTG 60.119 47.826 0.00 0.00 40.78 4.17
6012 7421 3.091545 GGTTGGTGATGTTGATCATGGT 58.908 45.455 0.00 0.00 40.78 3.55
6013 7422 3.090790 TGGTTGGTGATGTTGATCATGG 58.909 45.455 0.00 0.00 40.78 3.66
6014 7423 4.678622 CATGGTTGGTGATGTTGATCATG 58.321 43.478 0.00 0.00 40.78 3.07
6015 7424 3.131577 GCATGGTTGGTGATGTTGATCAT 59.868 43.478 0.00 0.00 40.78 2.45
6016 7425 2.492881 GCATGGTTGGTGATGTTGATCA 59.507 45.455 0.00 0.00 36.16 2.92
6017 7426 2.478370 CGCATGGTTGGTGATGTTGATC 60.478 50.000 0.00 0.00 0.00 2.92
6018 7427 1.473677 CGCATGGTTGGTGATGTTGAT 59.526 47.619 0.00 0.00 0.00 2.57
6034 7443 0.534877 TTGATAGGGAATGCGCGCAT 60.535 50.000 39.13 39.13 38.46 4.73
6049 7458 3.067461 GTCTAGGCGAGTGACAGATTGAT 59.933 47.826 0.00 0.00 0.00 2.57
6060 7469 0.824759 GGTCAATGGTCTAGGCGAGT 59.175 55.000 0.00 0.00 0.00 4.18
6080 7489 0.535335 ATAGTCACGGCCATGTTCGT 59.465 50.000 2.24 4.99 40.49 3.85
6189 7598 5.437289 TCTCGTGAACATTTTGCAAATCT 57.563 34.783 13.65 0.48 0.00 2.40


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

AutoCloner maintained by Alex Coulton.