Multiple sequence alignment - TraesCS1D01G085400

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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 TraesCS1D01G085400 chr1D 100.000 6026 0 0 1 6026 69790773 69784748 0.000000e+00 11129.0
1 TraesCS1D01G085400 chr1D 95.455 66 3 0 3300 3365 69787410 69787345 8.260000e-19 106.0
2 TraesCS1D01G085400 chr1D 95.455 66 3 0 3364 3429 69787474 69787409 8.260000e-19 106.0
3 TraesCS1D01G085400 chr1B 97.883 3543 62 8 26 3558 111372873 111369334 0.000000e+00 6115.0
4 TraesCS1D01G085400 chr1B 91.434 2253 98 36 3809 6026 111369337 111367145 0.000000e+00 3003.0
5 TraesCS1D01G085400 chr1B 92.557 309 22 1 1 309 111373365 111373058 5.540000e-120 442.0
6 TraesCS1D01G085400 chr1B 86.486 333 29 5 5710 6026 111366203 111365871 9.610000e-93 351.0
7 TraesCS1D01G085400 chr1B 93.939 66 4 0 3364 3429 111369600 111369535 3.840000e-17 100.0
8 TraesCS1D01G085400 chr1A 97.631 3081 51 13 205 3278 69395194 69392129 0.000000e+00 5265.0
9 TraesCS1D01G085400 chr1A 97.546 1345 30 1 3809 5150 69391780 69390436 0.000000e+00 2298.0
10 TraesCS1D01G085400 chr1A 88.995 418 13 7 5202 5608 69390116 69389721 2.520000e-133 486.0
11 TraesCS1D01G085400 chr1A 90.055 362 32 4 3 363 69395551 69395193 3.290000e-127 466.0
12 TraesCS1D01G085400 chr1A 95.222 293 6 4 3274 3558 69392069 69391777 1.980000e-124 457.0
13 TraesCS1D01G085400 chr1A 80.077 261 41 6 7 267 69397007 69396758 3.710000e-42 183.0
14 TraesCS1D01G085400 chr1A 92.424 66 5 0 3300 3365 69391979 69391914 1.790000e-15 95.3
15 TraesCS1D01G085400 chr4D 94.862 253 12 1 3557 3809 73779797 73780048 1.570000e-105 394.0
16 TraesCS1D01G085400 chr2A 94.094 254 14 1 3553 3806 549697069 549697321 9.470000e-103 385.0
17 TraesCS1D01G085400 chr6B 93.701 254 15 1 3559 3812 315567371 315567119 4.410000e-101 379.0
18 TraesCS1D01G085400 chr2D 93.050 259 16 2 3555 3813 513258851 513258595 1.590000e-100 377.0
19 TraesCS1D01G085400 chr5A 92.636 258 18 1 3555 3812 368940229 368940485 2.650000e-98 370.0
20 TraesCS1D01G085400 chr4A 93.548 248 15 1 3559 3806 194490363 194490117 9.540000e-98 368.0
21 TraesCS1D01G085400 chrUn 92.885 253 16 2 3557 3809 67654689 67654939 3.430000e-97 366.0
22 TraesCS1D01G085400 chr7A 92.248 258 19 1 3557 3814 413764526 413764782 1.230000e-96 364.0
23 TraesCS1D01G085400 chr4B 92.188 256 19 1 3558 3813 568332360 568332106 1.600000e-95 361.0


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 TraesCS1D01G085400 chr1D 69784748 69790773 6025 True 3780.333333 11129 96.970000 1 6026 3 chr1D.!!$R1 6025
1 TraesCS1D01G085400 chr1B 111365871 111373365 7494 True 2002.200000 6115 92.459800 1 6026 5 chr1B.!!$R1 6025
2 TraesCS1D01G085400 chr1A 69389721 69397007 7286 True 1321.471429 5265 91.707143 3 5608 7 chr1A.!!$R1 5605

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
473 2105 2.450476 CAAGGAAGAAGGGTGAATGGG 58.550 52.381 0.00 0.00 0.00 4.00 F
910 2544 2.781681 TCCCGTCCTTGGAGAATTTC 57.218 50.000 0.00 0.00 0.00 2.17 F
2337 3972 1.212935 ACTGGTACCATTGCCTCCATC 59.787 52.381 16.75 0.00 0.00 3.51 F
3578 5285 0.038310 GGCTGTTTGGTTCTAGGCCT 59.962 55.000 11.78 11.78 35.73 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 2959 0.042431 AGGATCTCCTCCAGCTGTGT 59.958 55.000 13.81 0.0 44.77 3.72 R
2909 4544 3.118482 TGAAAGCTCCACAAAATTTGCCA 60.118 39.130 5.52 0.0 0.00 4.92 R
3789 5496 0.032615 AGGGGCTGTTTGGTTTGTGA 60.033 50.000 0.00 0.0 0.00 3.58 R
5497 7487 1.227205 CAGGCAAGCACCGCAAAAA 60.227 52.632 0.00 0.0 33.69 1.94 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
97 1570 3.691342 TGTCCCACTTCCGAGCCG 61.691 66.667 0.00 0.00 0.00 5.52
112 1585 3.039202 GCCGATCCAAACACTGGCG 62.039 63.158 0.00 0.00 45.98 5.69
126 1599 4.538917 ACACTGGCGGTTTAAAATTAACG 58.461 39.130 0.00 0.00 0.00 3.18
178 1651 3.627395 AACCGATTAGACCATGCAGAA 57.373 42.857 0.00 0.00 0.00 3.02
179 1652 3.845781 ACCGATTAGACCATGCAGAAT 57.154 42.857 0.00 0.00 0.00 2.40
182 1655 3.070018 CGATTAGACCATGCAGAATCCC 58.930 50.000 0.00 0.00 0.00 3.85
473 2105 2.450476 CAAGGAAGAAGGGTGAATGGG 58.550 52.381 0.00 0.00 0.00 4.00
840 2474 8.504005 TCTCACAGTATTTTTCTCCGATTTTTC 58.496 33.333 0.00 0.00 0.00 2.29
910 2544 2.781681 TCCCGTCCTTGGAGAATTTC 57.218 50.000 0.00 0.00 0.00 2.17
947 2582 3.490348 CTGTTGGGAGATTTTCTGGTGT 58.510 45.455 0.00 0.00 0.00 4.16
2337 3972 1.212935 ACTGGTACCATTGCCTCCATC 59.787 52.381 16.75 0.00 0.00 3.51
2486 4121 6.647229 TGAATCATGATTCTAGTGCTGAAGT 58.353 36.000 36.15 8.03 45.55 3.01
2909 4544 2.356793 GCACGCAGCTGAGTCTGT 60.357 61.111 21.00 5.19 41.15 3.41
2910 4545 2.665395 GCACGCAGCTGAGTCTGTG 61.665 63.158 21.00 17.25 46.79 3.66
3025 4660 6.389830 TTGCATCTGAAAAGAGCAAACTAA 57.610 33.333 0.00 0.00 41.65 2.24
3106 4741 4.546829 ACAACCTTGCCTCTTCGTAATA 57.453 40.909 0.00 0.00 0.00 0.98
3210 4845 7.604927 GTGGTTTAGTTGACATATACTCCACAA 59.395 37.037 0.00 0.00 37.04 3.33
3453 5152 4.148891 CGTTTCGCTTCATGGTCTTTTAC 58.851 43.478 0.00 0.00 0.00 2.01
3564 5271 4.718961 CTGTAAGCATATTTAGGGGCTGT 58.281 43.478 0.00 0.00 36.58 4.40
3565 5272 5.124036 TGTAAGCATATTTAGGGGCTGTT 57.876 39.130 0.00 0.00 36.58 3.16
3566 5273 5.515106 TGTAAGCATATTTAGGGGCTGTTT 58.485 37.500 0.00 0.00 36.58 2.83
3567 5274 5.359576 TGTAAGCATATTTAGGGGCTGTTTG 59.640 40.000 0.00 0.00 36.58 2.93
3568 5275 3.299503 AGCATATTTAGGGGCTGTTTGG 58.700 45.455 0.00 0.00 34.83 3.28
3569 5276 3.031013 GCATATTTAGGGGCTGTTTGGT 58.969 45.455 0.00 0.00 0.00 3.67
3570 5277 3.450817 GCATATTTAGGGGCTGTTTGGTT 59.549 43.478 0.00 0.00 0.00 3.67
3571 5278 4.441495 GCATATTTAGGGGCTGTTTGGTTC 60.441 45.833 0.00 0.00 0.00 3.62
3572 5279 3.542969 ATTTAGGGGCTGTTTGGTTCT 57.457 42.857 0.00 0.00 0.00 3.01
3573 5280 4.668138 ATTTAGGGGCTGTTTGGTTCTA 57.332 40.909 0.00 0.00 0.00 2.10
3574 5281 3.713826 TTAGGGGCTGTTTGGTTCTAG 57.286 47.619 0.00 0.00 0.00 2.43
3575 5282 0.698818 AGGGGCTGTTTGGTTCTAGG 59.301 55.000 0.00 0.00 0.00 3.02
3576 5283 0.965866 GGGGCTGTTTGGTTCTAGGC 60.966 60.000 0.00 0.00 35.24 3.93
3577 5284 0.965866 GGGCTGTTTGGTTCTAGGCC 60.966 60.000 0.00 0.00 46.53 5.19
3578 5285 0.038310 GGCTGTTTGGTTCTAGGCCT 59.962 55.000 11.78 11.78 35.73 5.19
3579 5286 1.280998 GGCTGTTTGGTTCTAGGCCTA 59.719 52.381 13.09 13.09 35.73 3.93
3580 5287 2.633488 GCTGTTTGGTTCTAGGCCTAG 58.367 52.381 30.94 30.94 34.56 3.02
3581 5288 2.633488 CTGTTTGGTTCTAGGCCTAGC 58.367 52.381 31.76 19.82 33.32 3.42
3582 5289 1.982226 TGTTTGGTTCTAGGCCTAGCA 59.018 47.619 31.76 21.24 33.32 3.49
3583 5290 2.576191 TGTTTGGTTCTAGGCCTAGCAT 59.424 45.455 31.76 0.00 33.32 3.79
3584 5291 3.010138 TGTTTGGTTCTAGGCCTAGCATT 59.990 43.478 31.76 0.00 33.32 3.56
3585 5292 3.281727 TTGGTTCTAGGCCTAGCATTG 57.718 47.619 31.76 12.05 33.32 2.82
3586 5293 1.134098 TGGTTCTAGGCCTAGCATTGC 60.134 52.381 31.76 18.76 33.32 3.56
3591 5298 4.483090 GGCCTAGCATTGCCCTAC 57.517 61.111 4.70 0.00 41.97 3.18
3592 5299 1.839894 GGCCTAGCATTGCCCTACT 59.160 57.895 4.70 0.00 41.97 2.57
3593 5300 0.183731 GGCCTAGCATTGCCCTACTT 59.816 55.000 4.70 0.00 41.97 2.24
3594 5301 1.410224 GGCCTAGCATTGCCCTACTTT 60.410 52.381 4.70 0.00 41.97 2.66
3595 5302 2.379005 GCCTAGCATTGCCCTACTTTT 58.621 47.619 4.70 0.00 0.00 2.27
3596 5303 2.099756 GCCTAGCATTGCCCTACTTTTG 59.900 50.000 4.70 0.00 0.00 2.44
3597 5304 2.099756 CCTAGCATTGCCCTACTTTTGC 59.900 50.000 4.70 0.00 0.00 3.68
3598 5305 0.897621 AGCATTGCCCTACTTTTGCC 59.102 50.000 4.70 0.00 0.00 4.52
3599 5306 0.607620 GCATTGCCCTACTTTTGCCA 59.392 50.000 0.00 0.00 0.00 4.92
3600 5307 1.672737 GCATTGCCCTACTTTTGCCAC 60.673 52.381 0.00 0.00 0.00 5.01
3601 5308 1.617850 CATTGCCCTACTTTTGCCACA 59.382 47.619 0.00 0.00 0.00 4.17
3602 5309 1.036707 TTGCCCTACTTTTGCCACAC 58.963 50.000 0.00 0.00 0.00 3.82
3603 5310 0.106469 TGCCCTACTTTTGCCACACA 60.106 50.000 0.00 0.00 0.00 3.72
3604 5311 1.256812 GCCCTACTTTTGCCACACAT 58.743 50.000 0.00 0.00 0.00 3.21
3605 5312 1.618343 GCCCTACTTTTGCCACACATT 59.382 47.619 0.00 0.00 0.00 2.71
3606 5313 2.037121 GCCCTACTTTTGCCACACATTT 59.963 45.455 0.00 0.00 0.00 2.32
3607 5314 3.494223 GCCCTACTTTTGCCACACATTTT 60.494 43.478 0.00 0.00 0.00 1.82
3608 5315 4.702831 CCCTACTTTTGCCACACATTTTT 58.297 39.130 0.00 0.00 0.00 1.94
3609 5316 4.511082 CCCTACTTTTGCCACACATTTTTG 59.489 41.667 0.00 0.00 0.00 2.44
3610 5317 4.024977 CCTACTTTTGCCACACATTTTTGC 60.025 41.667 0.00 0.00 0.00 3.68
3611 5318 2.682352 ACTTTTGCCACACATTTTTGCC 59.318 40.909 0.00 0.00 0.00 4.52
3612 5319 2.408271 TTTGCCACACATTTTTGCCA 57.592 40.000 0.00 0.00 0.00 4.92
3613 5320 2.408271 TTGCCACACATTTTTGCCAA 57.592 40.000 0.00 0.00 0.00 4.52
3614 5321 1.950828 TGCCACACATTTTTGCCAAG 58.049 45.000 0.00 0.00 0.00 3.61
3615 5322 0.587768 GCCACACATTTTTGCCAAGC 59.412 50.000 0.00 0.00 0.00 4.01
3616 5323 1.811176 GCCACACATTTTTGCCAAGCT 60.811 47.619 0.00 0.00 0.00 3.74
3617 5324 2.563702 CCACACATTTTTGCCAAGCTT 58.436 42.857 0.00 0.00 0.00 3.74
3618 5325 2.288458 CCACACATTTTTGCCAAGCTTG 59.712 45.455 19.93 19.93 0.00 4.01
3619 5326 1.941975 ACACATTTTTGCCAAGCTTGC 59.058 42.857 21.43 16.17 0.00 4.01
3620 5327 1.264826 CACATTTTTGCCAAGCTTGCC 59.735 47.619 21.43 11.17 0.00 4.52
3621 5328 1.141455 ACATTTTTGCCAAGCTTGCCT 59.859 42.857 21.43 0.00 0.00 4.75
3622 5329 2.368221 ACATTTTTGCCAAGCTTGCCTA 59.632 40.909 21.43 3.89 0.00 3.93
3623 5330 3.181456 ACATTTTTGCCAAGCTTGCCTAA 60.181 39.130 21.43 10.63 0.00 2.69
3624 5331 2.818130 TTTTGCCAAGCTTGCCTAAG 57.182 45.000 21.43 8.08 36.97 2.18
3625 5332 0.968405 TTTGCCAAGCTTGCCTAAGG 59.032 50.000 21.43 7.42 34.40 2.69
3626 5333 0.178964 TTGCCAAGCTTGCCTAAGGT 60.179 50.000 21.43 0.00 45.98 3.50
3634 5341 4.367039 AGCTTGCCTAAGGTTAGTTCAA 57.633 40.909 0.00 0.48 41.61 2.69
3635 5342 4.072839 AGCTTGCCTAAGGTTAGTTCAAC 58.927 43.478 0.00 0.00 41.61 3.18
3636 5343 3.818773 GCTTGCCTAAGGTTAGTTCAACA 59.181 43.478 0.00 0.00 39.04 3.33
3637 5344 4.277423 GCTTGCCTAAGGTTAGTTCAACAA 59.723 41.667 0.00 0.00 39.04 2.83
3638 5345 5.221165 GCTTGCCTAAGGTTAGTTCAACAAA 60.221 40.000 0.00 0.00 39.04 2.83
3639 5346 6.681865 GCTTGCCTAAGGTTAGTTCAACAAAA 60.682 38.462 0.00 0.00 39.04 2.44
3640 5347 6.969993 TGCCTAAGGTTAGTTCAACAAAAT 57.030 33.333 0.00 0.00 39.04 1.82
3641 5348 6.744112 TGCCTAAGGTTAGTTCAACAAAATG 58.256 36.000 0.00 0.00 39.04 2.32
3642 5349 6.547880 TGCCTAAGGTTAGTTCAACAAAATGA 59.452 34.615 0.00 0.00 39.04 2.57
3643 5350 7.084486 GCCTAAGGTTAGTTCAACAAAATGAG 58.916 38.462 0.00 0.00 39.04 2.90
3644 5351 7.040686 GCCTAAGGTTAGTTCAACAAAATGAGA 60.041 37.037 0.00 0.00 39.04 3.27
3645 5352 8.507249 CCTAAGGTTAGTTCAACAAAATGAGAG 58.493 37.037 0.00 0.00 39.04 3.20
3646 5353 6.319141 AGGTTAGTTCAACAAAATGAGAGC 57.681 37.500 0.00 0.00 39.04 4.09
3647 5354 5.241728 AGGTTAGTTCAACAAAATGAGAGCC 59.758 40.000 0.00 0.00 39.04 4.70
3648 5355 5.009610 GGTTAGTTCAACAAAATGAGAGCCA 59.990 40.000 0.00 0.00 39.04 4.75
3649 5356 4.574599 AGTTCAACAAAATGAGAGCCAC 57.425 40.909 0.00 0.00 0.00 5.01
3650 5357 3.953612 AGTTCAACAAAATGAGAGCCACA 59.046 39.130 0.00 0.00 0.00 4.17
3651 5358 4.402155 AGTTCAACAAAATGAGAGCCACAA 59.598 37.500 0.00 0.00 0.00 3.33
3652 5359 4.572985 TCAACAAAATGAGAGCCACAAG 57.427 40.909 0.00 0.00 0.00 3.16
3653 5360 3.953612 TCAACAAAATGAGAGCCACAAGT 59.046 39.130 0.00 0.00 0.00 3.16
3654 5361 4.402155 TCAACAAAATGAGAGCCACAAGTT 59.598 37.500 0.00 0.00 0.00 2.66
3655 5362 4.311816 ACAAAATGAGAGCCACAAGTTG 57.688 40.909 0.00 0.00 0.00 3.16
3663 5370 3.860681 CCACAAGTTGGCAAGCCT 58.139 55.556 12.96 0.00 39.07 4.58
3664 5371 3.034924 CCACAAGTTGGCAAGCCTA 57.965 52.632 12.96 1.22 39.07 3.93
3665 5372 1.327303 CCACAAGTTGGCAAGCCTAA 58.673 50.000 12.96 2.46 39.07 2.69
3666 5373 1.270550 CCACAAGTTGGCAAGCCTAAG 59.729 52.381 12.96 1.51 39.07 2.18
3667 5374 1.270550 CACAAGTTGGCAAGCCTAAGG 59.729 52.381 12.96 0.79 36.94 2.69
3668 5375 0.890683 CAAGTTGGCAAGCCTAAGGG 59.109 55.000 12.96 0.00 36.94 3.95
3669 5376 0.777446 AAGTTGGCAAGCCTAAGGGA 59.223 50.000 12.96 0.00 36.94 4.20
3670 5377 0.777446 AGTTGGCAAGCCTAAGGGAA 59.223 50.000 12.96 0.00 36.94 3.97
3671 5378 1.359130 AGTTGGCAAGCCTAAGGGAAT 59.641 47.619 12.96 0.00 36.94 3.01
3672 5379 1.751351 GTTGGCAAGCCTAAGGGAATC 59.249 52.381 12.96 0.00 36.94 2.52
3673 5380 1.298953 TGGCAAGCCTAAGGGAATCT 58.701 50.000 12.96 0.00 36.94 2.40
3674 5381 1.640670 TGGCAAGCCTAAGGGAATCTT 59.359 47.619 12.96 0.00 39.40 2.40
3675 5382 2.027385 GGCAAGCCTAAGGGAATCTTG 58.973 52.381 3.29 0.00 36.93 3.02
3676 5383 1.406898 GCAAGCCTAAGGGAATCTTGC 59.593 52.381 13.14 13.14 43.47 4.01
3677 5384 2.027385 CAAGCCTAAGGGAATCTTGCC 58.973 52.381 0.00 0.00 39.23 4.52
3678 5385 1.298953 AGCCTAAGGGAATCTTGCCA 58.701 50.000 3.19 0.00 41.75 4.92
3679 5386 1.064389 AGCCTAAGGGAATCTTGCCAC 60.064 52.381 3.19 0.00 41.75 5.01
3680 5387 1.340991 GCCTAAGGGAATCTTGCCACA 60.341 52.381 3.19 0.00 41.75 4.17
3681 5388 2.369394 CCTAAGGGAATCTTGCCACAC 58.631 52.381 3.19 0.00 41.75 3.82
3682 5389 2.025887 CCTAAGGGAATCTTGCCACACT 60.026 50.000 3.19 0.00 41.75 3.55
3683 5390 2.683211 AAGGGAATCTTGCCACACTT 57.317 45.000 3.19 0.00 41.75 3.16
3684 5391 2.683211 AGGGAATCTTGCCACACTTT 57.317 45.000 3.19 0.00 41.75 2.66
3685 5392 2.962859 AGGGAATCTTGCCACACTTTT 58.037 42.857 3.19 0.00 41.75 2.27
3686 5393 3.308401 AGGGAATCTTGCCACACTTTTT 58.692 40.909 3.19 0.00 41.75 1.94
3687 5394 3.070015 AGGGAATCTTGCCACACTTTTTG 59.930 43.478 3.19 0.00 41.75 2.44
3688 5395 3.181466 GGGAATCTTGCCACACTTTTTGT 60.181 43.478 0.00 0.00 39.97 2.83
3689 5396 8.796649 AAGGGAATCTTGCCACACTTTTTGTG 62.797 42.308 3.19 0.00 43.76 3.33
3701 5408 4.619973 CACTTTTTGTGTGTATGCCATGT 58.380 39.130 0.00 0.00 41.53 3.21
3702 5409 4.445052 CACTTTTTGTGTGTATGCCATGTG 59.555 41.667 0.00 0.00 41.53 3.21
3703 5410 3.657015 TTTTGTGTGTATGCCATGTGG 57.343 42.857 0.00 0.00 38.53 4.17
3704 5411 1.543607 TTGTGTGTATGCCATGTGGG 58.456 50.000 0.54 0.00 40.85 4.61
3705 5412 0.323269 TGTGTGTATGCCATGTGGGG 60.323 55.000 0.54 0.00 37.04 4.96
3713 5420 2.681064 CCATGTGGGGCCCAAGTG 60.681 66.667 30.70 26.87 34.18 3.16
3714 5421 2.118076 CATGTGGGGCCCAAGTGT 59.882 61.111 30.70 10.84 34.18 3.55
3715 5422 2.118076 ATGTGGGGCCCAAGTGTG 59.882 61.111 30.70 0.00 34.18 3.82
3716 5423 3.528217 ATGTGGGGCCCAAGTGTGG 62.528 63.158 30.70 0.00 45.53 4.17
3728 5435 2.959507 AAGTGTGGCTTGAACCAAAC 57.040 45.000 0.00 0.00 46.81 2.93
3730 5437 1.921243 GTGTGGCTTGAACCAAACAC 58.079 50.000 0.00 0.00 45.87 3.32
3731 5438 1.476488 GTGTGGCTTGAACCAAACACT 59.524 47.619 0.00 0.00 45.87 3.55
3732 5439 1.748493 TGTGGCTTGAACCAAACACTC 59.252 47.619 12.25 0.00 42.70 3.51
3733 5440 1.748493 GTGGCTTGAACCAAACACTCA 59.252 47.619 0.00 0.00 42.70 3.41
3734 5441 1.748493 TGGCTTGAACCAAACACTCAC 59.252 47.619 0.00 0.00 36.55 3.51
3735 5442 1.067060 GGCTTGAACCAAACACTCACC 59.933 52.381 0.00 0.00 0.00 4.02
3736 5443 2.024414 GCTTGAACCAAACACTCACCT 58.976 47.619 0.00 0.00 0.00 4.00
3737 5444 3.211045 GCTTGAACCAAACACTCACCTA 58.789 45.455 0.00 0.00 0.00 3.08
3738 5445 3.630312 GCTTGAACCAAACACTCACCTAA 59.370 43.478 0.00 0.00 0.00 2.69
3739 5446 4.261197 GCTTGAACCAAACACTCACCTAAG 60.261 45.833 0.00 0.00 0.00 2.18
3740 5447 4.497291 TGAACCAAACACTCACCTAAGT 57.503 40.909 0.00 0.00 0.00 2.24
3741 5448 4.850680 TGAACCAAACACTCACCTAAGTT 58.149 39.130 0.00 0.00 0.00 2.66
3742 5449 4.638421 TGAACCAAACACTCACCTAAGTTG 59.362 41.667 0.00 0.00 0.00 3.16
3743 5450 4.497291 ACCAAACACTCACCTAAGTTGA 57.503 40.909 0.00 0.00 0.00 3.18
3744 5451 5.048846 ACCAAACACTCACCTAAGTTGAT 57.951 39.130 0.00 0.00 0.00 2.57
3745 5452 5.063880 ACCAAACACTCACCTAAGTTGATC 58.936 41.667 0.00 0.00 0.00 2.92
3746 5453 5.063204 CCAAACACTCACCTAAGTTGATCA 58.937 41.667 0.00 0.00 0.00 2.92
3747 5454 5.530915 CCAAACACTCACCTAAGTTGATCAA 59.469 40.000 3.38 3.38 0.00 2.57
3748 5455 6.039270 CCAAACACTCACCTAAGTTGATCAAA 59.961 38.462 10.35 0.00 0.00 2.69
3749 5456 6.619801 AACACTCACCTAAGTTGATCAAAC 57.380 37.500 10.35 4.88 39.24 2.93
3777 5484 7.745620 CCTAAGTTTAGGTGTGACAATCTTT 57.254 36.000 9.36 0.00 44.26 2.52
3778 5485 7.584987 CCTAAGTTTAGGTGTGACAATCTTTG 58.415 38.462 9.36 0.00 44.26 2.77
3779 5486 6.391227 AAGTTTAGGTGTGACAATCTTTGG 57.609 37.500 0.00 0.00 34.12 3.28
3780 5487 4.278419 AGTTTAGGTGTGACAATCTTTGGC 59.722 41.667 0.00 0.00 39.85 4.52
3791 5498 6.072112 GACAATCTTTGGCAAAGTTAGTCA 57.928 37.500 31.49 20.18 38.99 3.41
3792 5499 5.831997 ACAATCTTTGGCAAAGTTAGTCAC 58.168 37.500 32.46 0.00 39.52 3.67
3793 5500 5.359576 ACAATCTTTGGCAAAGTTAGTCACA 59.640 36.000 32.46 16.01 39.52 3.58
3794 5501 6.127479 ACAATCTTTGGCAAAGTTAGTCACAA 60.127 34.615 32.46 15.37 39.52 3.33
3795 5502 5.906113 TCTTTGGCAAAGTTAGTCACAAA 57.094 34.783 32.46 12.18 39.52 2.83
3796 5503 5.646606 TCTTTGGCAAAGTTAGTCACAAAC 58.353 37.500 32.46 0.00 39.52 2.93
3797 5504 4.379339 TTGGCAAAGTTAGTCACAAACC 57.621 40.909 0.00 0.00 0.00 3.27
3798 5505 3.357203 TGGCAAAGTTAGTCACAAACCA 58.643 40.909 0.00 0.00 0.00 3.67
3799 5506 3.764434 TGGCAAAGTTAGTCACAAACCAA 59.236 39.130 0.00 0.00 0.00 3.67
3800 5507 4.220821 TGGCAAAGTTAGTCACAAACCAAA 59.779 37.500 0.00 0.00 0.00 3.28
3801 5508 4.565166 GGCAAAGTTAGTCACAAACCAAAC 59.435 41.667 0.00 0.00 0.00 2.93
3802 5509 5.164954 GCAAAGTTAGTCACAAACCAAACA 58.835 37.500 0.00 0.00 30.35 2.83
3803 5510 5.288472 GCAAAGTTAGTCACAAACCAAACAG 59.712 40.000 0.00 0.00 30.35 3.16
3804 5511 4.632538 AGTTAGTCACAAACCAAACAGC 57.367 40.909 0.00 0.00 30.35 4.40
3805 5512 3.380320 AGTTAGTCACAAACCAAACAGCC 59.620 43.478 0.00 0.00 30.35 4.85
3806 5513 1.111277 AGTCACAAACCAAACAGCCC 58.889 50.000 0.00 0.00 0.00 5.19
3807 5514 0.104120 GTCACAAACCAAACAGCCCC 59.896 55.000 0.00 0.00 0.00 5.80
3888 5595 6.817184 TCTATTCTTCATTAAACTCCTCCCG 58.183 40.000 0.00 0.00 0.00 5.14
3988 5695 3.387397 ACAGAGTAAAAAGTCGGTTCCG 58.613 45.455 4.74 4.74 0.00 4.30
4141 5848 5.192927 ACAGGAAATGACTTGTGTCTTTCA 58.807 37.500 15.54 0.00 43.29 2.69
4201 5908 4.081586 GTGGCTTAGGTTAGACTGCTACTT 60.082 45.833 0.00 0.00 0.00 2.24
4218 5925 6.414732 TGCTACTTAAACCAGCATCATAAGT 58.585 36.000 0.00 0.00 40.26 2.24
4357 6064 3.492421 AGCTTTCATGGTTTGCATACG 57.508 42.857 1.02 0.00 0.00 3.06
4497 6204 2.557924 TGTTGAATGCTTGCAGGTAAGG 59.442 45.455 0.87 0.00 0.00 2.69
4524 6231 1.760029 CAGGAAGAGGCTAGGAAGACC 59.240 57.143 0.00 0.00 0.00 3.85
5004 6711 3.005539 ATCCAGCGCAGGGTCTGT 61.006 61.111 19.70 0.00 33.43 3.41
5244 7224 0.035056 CCCTCCCTGTGGATTGTGTC 60.035 60.000 0.00 0.00 40.80 3.67
5245 7225 0.692476 CCTCCCTGTGGATTGTGTCA 59.308 55.000 0.00 0.00 40.80 3.58
5246 7226 1.283029 CCTCCCTGTGGATTGTGTCAT 59.717 52.381 0.00 0.00 40.80 3.06
5247 7227 2.291153 CCTCCCTGTGGATTGTGTCATT 60.291 50.000 0.00 0.00 40.80 2.57
5248 7228 2.751259 CTCCCTGTGGATTGTGTCATTG 59.249 50.000 0.00 0.00 40.80 2.82
5249 7229 2.108075 TCCCTGTGGATTGTGTCATTGT 59.892 45.455 0.00 0.00 35.03 2.71
5250 7230 2.229543 CCCTGTGGATTGTGTCATTGTG 59.770 50.000 0.00 0.00 0.00 3.33
5251 7231 2.886523 CCTGTGGATTGTGTCATTGTGT 59.113 45.455 0.00 0.00 0.00 3.72
5378 7368 1.867595 AAGGGAATGGGAGCCACAGG 61.868 60.000 0.00 0.00 35.80 4.00
5450 7440 0.744414 TGAGCTTGCCGGAATACTGC 60.744 55.000 5.05 0.00 0.00 4.40
5453 7443 1.312371 GCTTGCCGGAATACTGCCAA 61.312 55.000 5.05 0.00 0.00 4.52
5468 7458 8.772844 GAATACTGCCAACCATGGGTATTCTTT 61.773 40.741 26.15 8.33 45.58 2.52
5488 7478 4.385358 TTGCTGGAGTTGTTTCCTTTTC 57.615 40.909 0.00 0.00 38.12 2.29
5489 7479 2.357637 TGCTGGAGTTGTTTCCTTTTCG 59.642 45.455 0.00 0.00 38.12 3.46
5490 7480 2.858646 GCTGGAGTTGTTTCCTTTTCGC 60.859 50.000 0.00 0.00 38.12 4.70
5491 7481 1.679153 TGGAGTTGTTTCCTTTTCGCC 59.321 47.619 0.00 0.00 38.12 5.54
5492 7482 1.954382 GGAGTTGTTTCCTTTTCGCCT 59.046 47.619 0.00 0.00 34.27 5.52
5493 7483 2.361119 GGAGTTGTTTCCTTTTCGCCTT 59.639 45.455 0.00 0.00 34.27 4.35
5494 7484 3.550233 GGAGTTGTTTCCTTTTCGCCTTC 60.550 47.826 0.00 0.00 34.27 3.46
5495 7485 2.361119 AGTTGTTTCCTTTTCGCCTTCC 59.639 45.455 0.00 0.00 0.00 3.46
5496 7486 2.358322 TGTTTCCTTTTCGCCTTCCT 57.642 45.000 0.00 0.00 0.00 3.36
5497 7487 2.661718 TGTTTCCTTTTCGCCTTCCTT 58.338 42.857 0.00 0.00 0.00 3.36
5498 7488 3.028130 TGTTTCCTTTTCGCCTTCCTTT 58.972 40.909 0.00 0.00 0.00 3.11
5499 7489 3.449377 TGTTTCCTTTTCGCCTTCCTTTT 59.551 39.130 0.00 0.00 0.00 2.27
5547 7537 2.819595 AAGCGCGGAATGCACGAT 60.820 55.556 8.83 0.00 46.97 3.73
5608 7598 1.066143 ACTGTCGCCACAAGGATTAGG 60.066 52.381 0.00 0.00 36.89 2.69
5616 7606 3.181439 GCCACAAGGATTAGGGATTAGCT 60.181 47.826 0.00 0.00 36.89 3.32
5624 7614 4.699257 GGATTAGGGATTAGCTCAATGCAG 59.301 45.833 0.00 0.00 45.94 4.41
5636 7626 1.002366 CAATGCAGTCGGCTCTACAC 58.998 55.000 0.00 0.00 45.15 2.90
5638 7628 0.972983 ATGCAGTCGGCTCTACACCT 60.973 55.000 0.00 0.00 45.15 4.00
5639 7629 1.153745 GCAGTCGGCTCTACACCTG 60.154 63.158 0.00 0.00 40.25 4.00
5641 7631 0.965866 CAGTCGGCTCTACACCTGGA 60.966 60.000 0.00 0.00 0.00 3.86
5644 7634 0.259065 TCGGCTCTACACCTGGAGAT 59.741 55.000 0.00 0.00 0.00 2.75
5645 7635 0.387202 CGGCTCTACACCTGGAGATG 59.613 60.000 0.00 0.00 0.00 2.90
5646 7636 0.755686 GGCTCTACACCTGGAGATGG 59.244 60.000 0.00 0.00 0.00 3.51
5647 7637 1.490574 GCTCTACACCTGGAGATGGT 58.509 55.000 0.00 0.00 38.53 3.55
5648 7638 1.410882 GCTCTACACCTGGAGATGGTC 59.589 57.143 0.00 0.00 35.28 4.02
5649 7639 2.739943 CTCTACACCTGGAGATGGTCA 58.260 52.381 0.00 0.00 35.28 4.02
5653 7643 0.036010 CACCTGGAGATGGTCACACC 60.036 60.000 0.00 0.00 39.22 4.16
5662 7652 1.229051 TGGTCACACCATCGGGAGA 60.229 57.895 0.00 0.00 44.79 3.71
5664 7654 1.258445 GGTCACACCATCGGGAGAGT 61.258 60.000 0.00 0.00 45.48 3.24
5665 7655 1.471119 GTCACACCATCGGGAGAGTA 58.529 55.000 0.00 0.00 45.48 2.59
5666 7656 1.134560 GTCACACCATCGGGAGAGTAC 59.865 57.143 0.00 0.00 45.48 2.73
5668 7658 1.065928 CACCATCGGGAGAGTACGC 59.934 63.158 0.00 0.00 45.48 4.42
5669 7659 1.076923 ACCATCGGGAGAGTACGCT 60.077 57.895 0.00 0.00 45.48 5.07
5678 7672 1.983196 GAGAGTACGCTGCGAGCTCA 61.983 60.000 32.67 13.90 39.60 4.26
5679 7673 1.585002 GAGTACGCTGCGAGCTCAG 60.585 63.158 30.47 6.28 39.60 3.35
5686 7680 4.724602 TGCGAGCTCAGTCACGGC 62.725 66.667 15.40 7.55 0.00 5.68
5707 7701 2.509111 CAGCTGCATACGTCGCCA 60.509 61.111 0.00 0.00 0.00 5.69
5708 7702 2.202797 AGCTGCATACGTCGCCAG 60.203 61.111 1.02 6.23 0.00 4.85
5709 7703 3.264897 GCTGCATACGTCGCCAGG 61.265 66.667 7.36 0.00 0.00 4.45
5711 7705 3.723235 CTGCATACGTCGCCAGGCT 62.723 63.158 10.54 0.00 0.00 4.58
5715 7709 2.707849 ATACGTCGCCAGGCTTCGT 61.708 57.895 25.97 25.97 38.44 3.85
5760 7754 1.156736 GCGGCTAGAGAAACTTGCAA 58.843 50.000 0.00 0.00 46.11 4.08
5763 7757 3.814945 CGGCTAGAGAAACTTGCAAAAG 58.185 45.455 0.00 0.00 46.11 2.27
5765 7759 3.004734 GGCTAGAGAAACTTGCAAAAGCA 59.995 43.478 0.00 0.00 46.11 3.91
5788 7782 0.179020 TGACTGGTTGCAGGTGAAGG 60.179 55.000 0.00 0.00 0.00 3.46
5795 7789 0.538057 TTGCAGGTGAAGGCTTCAGG 60.538 55.000 29.22 21.26 41.01 3.86
5813 7807 0.038526 GGTCCGACGACAAGTGACAT 60.039 55.000 0.00 0.00 41.13 3.06
5866 7875 2.912366 CGGGTTAAAAAGTGCTTCGAC 58.088 47.619 0.00 0.00 0.00 4.20
5867 7876 2.288458 CGGGTTAAAAAGTGCTTCGACA 59.712 45.455 0.00 0.00 0.00 4.35
5870 7879 3.242511 GGTTAAAAAGTGCTTCGACACGT 60.243 43.478 0.98 0.00 45.45 4.49
5889 7898 2.671070 CGTGGTCATTGTCATCTCACGA 60.671 50.000 7.08 0.00 46.03 4.35
5891 7900 3.369147 GTGGTCATTGTCATCTCACGAAG 59.631 47.826 0.00 0.00 0.00 3.79
5906 7915 3.673338 TCACGAAGTCTATGAAAGCAACG 59.327 43.478 0.00 0.00 41.61 4.10
5907 7916 3.428870 CACGAAGTCTATGAAAGCAACGT 59.571 43.478 0.00 0.00 41.61 3.99
5911 7920 5.511088 AAGTCTATGAAAGCAACGTAACG 57.489 39.130 0.00 0.00 0.00 3.18
5929 7938 1.608590 ACGCAAGGGTGTTCTCAAATG 59.391 47.619 0.00 0.00 46.39 2.32
5930 7939 1.068333 CGCAAGGGTGTTCTCAAATGG 60.068 52.381 0.00 0.00 0.00 3.16
5950 7959 4.086457 TGGAGACTAGCACTATTGTGTCA 58.914 43.478 9.05 0.00 45.44 3.58
6000 8009 1.194781 TGAGGACTTGGAGGAGTGCC 61.195 60.000 0.00 0.00 38.60 5.01
6010 8019 3.660111 GGAGTGCCGGTGTTGTGC 61.660 66.667 1.90 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.337074 CCACGACGTTTAGGGTTAGCA 60.337 52.381 0.00 0.00 0.00 3.49
110 1583 3.734735 TGCAACCGTTAATTTTAAACCGC 59.265 39.130 0.00 0.00 0.00 5.68
112 1585 4.739228 ACGTGCAACCGTTAATTTTAAACC 59.261 37.500 0.00 0.00 37.96 3.27
473 2105 3.075641 GACGAGGGAGGGGTCACC 61.076 72.222 0.00 0.00 40.67 4.02
910 2544 1.318576 ACAGCCAAAGAAACGAAGGG 58.681 50.000 0.00 0.00 0.00 3.95
947 2582 5.818336 TCAAGTAATTCACCAACAGAAACGA 59.182 36.000 0.00 0.00 0.00 3.85
1324 2959 0.042431 AGGATCTCCTCCAGCTGTGT 59.958 55.000 13.81 0.00 44.77 3.72
2486 4121 3.780804 TTTTGCTGCTAGGGTCTACAA 57.219 42.857 0.00 0.00 0.00 2.41
2909 4544 3.118482 TGAAAGCTCCACAAAATTTGCCA 60.118 39.130 5.52 0.00 0.00 4.92
2910 4545 3.465871 TGAAAGCTCCACAAAATTTGCC 58.534 40.909 5.52 0.00 0.00 4.52
3025 4660 0.180406 AGTTGTTGCTGAACCCGAGT 59.820 50.000 0.00 0.00 0.00 4.18
3459 5165 8.845227 TCATTAGTATGCACAGAAACAGAAAAA 58.155 29.630 0.00 0.00 0.00 1.94
3554 5261 2.307686 CCTAGAACCAAACAGCCCCTAA 59.692 50.000 0.00 0.00 0.00 2.69
3555 5262 1.913419 CCTAGAACCAAACAGCCCCTA 59.087 52.381 0.00 0.00 0.00 3.53
3556 5263 0.698818 CCTAGAACCAAACAGCCCCT 59.301 55.000 0.00 0.00 0.00 4.79
3557 5264 0.965866 GCCTAGAACCAAACAGCCCC 60.966 60.000 0.00 0.00 0.00 5.80
3558 5265 0.965866 GGCCTAGAACCAAACAGCCC 60.966 60.000 0.00 0.00 32.68 5.19
3559 5266 0.038310 AGGCCTAGAACCAAACAGCC 59.962 55.000 1.29 0.00 39.25 4.85
3560 5267 2.633488 CTAGGCCTAGAACCAAACAGC 58.367 52.381 32.79 0.00 35.21 4.40
3561 5268 2.027192 TGCTAGGCCTAGAACCAAACAG 60.027 50.000 38.74 15.24 35.21 3.16
3562 5269 1.982226 TGCTAGGCCTAGAACCAAACA 59.018 47.619 38.74 23.41 35.21 2.83
3563 5270 2.781681 TGCTAGGCCTAGAACCAAAC 57.218 50.000 38.74 21.26 35.21 2.93
3564 5271 3.620488 CAATGCTAGGCCTAGAACCAAA 58.380 45.455 38.74 18.21 35.21 3.28
3565 5272 2.683742 GCAATGCTAGGCCTAGAACCAA 60.684 50.000 38.74 19.81 35.21 3.67
3566 5273 1.134098 GCAATGCTAGGCCTAGAACCA 60.134 52.381 38.74 27.60 35.21 3.67
3567 5274 1.598882 GCAATGCTAGGCCTAGAACC 58.401 55.000 38.74 23.28 35.21 3.62
3568 5275 1.598882 GGCAATGCTAGGCCTAGAAC 58.401 55.000 38.74 23.96 46.74 3.01
3575 5282 2.058593 AAAGTAGGGCAATGCTAGGC 57.941 50.000 4.82 0.00 0.00 3.93
3576 5283 2.099756 GCAAAAGTAGGGCAATGCTAGG 59.900 50.000 4.82 0.00 0.00 3.02
3577 5284 2.099756 GGCAAAAGTAGGGCAATGCTAG 59.900 50.000 4.82 0.00 34.37 3.42
3578 5285 2.099405 GGCAAAAGTAGGGCAATGCTA 58.901 47.619 4.82 0.00 34.37 3.49
3579 5286 0.897621 GGCAAAAGTAGGGCAATGCT 59.102 50.000 4.82 0.00 34.37 3.79
3580 5287 0.607620 TGGCAAAAGTAGGGCAATGC 59.392 50.000 0.00 0.00 36.57 3.56
3581 5288 1.617850 TGTGGCAAAAGTAGGGCAATG 59.382 47.619 0.00 0.00 41.51 2.82
3582 5289 1.618343 GTGTGGCAAAAGTAGGGCAAT 59.382 47.619 0.00 0.00 41.51 3.56
3583 5290 1.036707 GTGTGGCAAAAGTAGGGCAA 58.963 50.000 0.00 0.00 41.51 4.52
3584 5291 0.106469 TGTGTGGCAAAAGTAGGGCA 60.106 50.000 0.00 0.00 37.23 5.36
3585 5292 1.256812 ATGTGTGGCAAAAGTAGGGC 58.743 50.000 0.00 0.00 0.00 5.19
3586 5293 4.335400 AAAATGTGTGGCAAAAGTAGGG 57.665 40.909 0.00 0.00 0.00 3.53
3587 5294 4.024977 GCAAAAATGTGTGGCAAAAGTAGG 60.025 41.667 0.00 0.00 0.00 3.18
3588 5295 4.024977 GGCAAAAATGTGTGGCAAAAGTAG 60.025 41.667 0.00 0.00 39.93 2.57
3589 5296 3.873952 GGCAAAAATGTGTGGCAAAAGTA 59.126 39.130 0.00 0.00 39.93 2.24
3590 5297 2.682352 GGCAAAAATGTGTGGCAAAAGT 59.318 40.909 0.00 0.00 39.93 2.66
3591 5298 2.681848 TGGCAAAAATGTGTGGCAAAAG 59.318 40.909 0.00 0.00 46.13 2.27
3592 5299 2.715046 TGGCAAAAATGTGTGGCAAAA 58.285 38.095 0.00 0.00 46.13 2.44
3593 5300 2.408271 TGGCAAAAATGTGTGGCAAA 57.592 40.000 0.00 0.00 46.13 3.68
3596 5303 0.587768 GCTTGGCAAAAATGTGTGGC 59.412 50.000 0.00 0.00 40.55 5.01
3597 5304 2.243602 AGCTTGGCAAAAATGTGTGG 57.756 45.000 0.00 0.00 0.00 4.17
3598 5305 2.286536 GCAAGCTTGGCAAAAATGTGTG 60.287 45.455 27.10 0.00 0.00 3.82
3599 5306 1.941975 GCAAGCTTGGCAAAAATGTGT 59.058 42.857 27.10 0.00 0.00 3.72
3600 5307 2.673976 GCAAGCTTGGCAAAAATGTG 57.326 45.000 27.10 0.00 0.00 3.21
3610 5317 3.073274 ACTAACCTTAGGCAAGCTTGG 57.927 47.619 27.10 12.37 35.08 3.61
3611 5318 4.072131 TGAACTAACCTTAGGCAAGCTTG 58.928 43.478 22.44 22.44 35.08 4.01
3612 5319 4.367039 TGAACTAACCTTAGGCAAGCTT 57.633 40.909 0.00 0.00 35.08 3.74
3613 5320 4.072839 GTTGAACTAACCTTAGGCAAGCT 58.927 43.478 0.00 0.00 33.19 3.74
3614 5321 3.818773 TGTTGAACTAACCTTAGGCAAGC 59.181 43.478 0.00 0.00 38.55 4.01
3615 5322 6.385649 TTTGTTGAACTAACCTTAGGCAAG 57.614 37.500 0.00 0.00 38.55 4.01
3616 5323 6.777213 TTTTGTTGAACTAACCTTAGGCAA 57.223 33.333 0.00 0.00 38.55 4.52
3617 5324 6.547880 TCATTTTGTTGAACTAACCTTAGGCA 59.452 34.615 0.00 0.00 38.55 4.75
3618 5325 6.977213 TCATTTTGTTGAACTAACCTTAGGC 58.023 36.000 0.00 0.00 38.55 3.93
3619 5326 8.391075 TCTCATTTTGTTGAACTAACCTTAGG 57.609 34.615 0.00 0.00 38.55 2.69
3620 5327 8.017946 GCTCTCATTTTGTTGAACTAACCTTAG 58.982 37.037 0.00 0.00 38.55 2.18
3621 5328 7.040686 GGCTCTCATTTTGTTGAACTAACCTTA 60.041 37.037 0.00 0.00 38.55 2.69
3622 5329 6.239036 GGCTCTCATTTTGTTGAACTAACCTT 60.239 38.462 0.00 0.00 38.55 3.50
3623 5330 5.241728 GGCTCTCATTTTGTTGAACTAACCT 59.758 40.000 0.00 0.00 38.55 3.50
3624 5331 5.009610 TGGCTCTCATTTTGTTGAACTAACC 59.990 40.000 0.00 0.00 38.55 2.85
3625 5332 5.915196 GTGGCTCTCATTTTGTTGAACTAAC 59.085 40.000 0.00 0.00 39.80 2.34
3626 5333 5.592282 TGTGGCTCTCATTTTGTTGAACTAA 59.408 36.000 0.00 0.00 0.00 2.24
3627 5334 5.129634 TGTGGCTCTCATTTTGTTGAACTA 58.870 37.500 0.00 0.00 0.00 2.24
3628 5335 3.953612 TGTGGCTCTCATTTTGTTGAACT 59.046 39.130 0.00 0.00 0.00 3.01
3629 5336 4.305989 TGTGGCTCTCATTTTGTTGAAC 57.694 40.909 0.00 0.00 0.00 3.18
3630 5337 4.402155 ACTTGTGGCTCTCATTTTGTTGAA 59.598 37.500 0.00 0.00 0.00 2.69
3631 5338 3.953612 ACTTGTGGCTCTCATTTTGTTGA 59.046 39.130 0.00 0.00 0.00 3.18
3632 5339 4.311816 ACTTGTGGCTCTCATTTTGTTG 57.688 40.909 0.00 0.00 0.00 3.33
3633 5340 4.441913 CCAACTTGTGGCTCTCATTTTGTT 60.442 41.667 0.00 0.00 41.72 2.83
3634 5341 3.068590 CCAACTTGTGGCTCTCATTTTGT 59.931 43.478 0.00 0.00 41.72 2.83
3635 5342 3.645884 CCAACTTGTGGCTCTCATTTTG 58.354 45.455 0.00 0.00 41.72 2.44
3647 5354 1.270550 CCTTAGGCTTGCCAACTTGTG 59.729 52.381 14.54 0.00 0.00 3.33
3648 5355 1.620822 CCTTAGGCTTGCCAACTTGT 58.379 50.000 14.54 0.00 0.00 3.16
3649 5356 0.890683 CCCTTAGGCTTGCCAACTTG 59.109 55.000 14.54 0.00 0.00 3.16
3650 5357 0.777446 TCCCTTAGGCTTGCCAACTT 59.223 50.000 14.54 0.00 0.00 2.66
3651 5358 0.777446 TTCCCTTAGGCTTGCCAACT 59.223 50.000 14.54 0.00 0.00 3.16
3652 5359 1.751351 GATTCCCTTAGGCTTGCCAAC 59.249 52.381 14.54 0.00 0.00 3.77
3653 5360 1.640670 AGATTCCCTTAGGCTTGCCAA 59.359 47.619 14.54 5.54 0.00 4.52
3654 5361 1.298953 AGATTCCCTTAGGCTTGCCA 58.701 50.000 14.54 0.00 0.00 4.92
3655 5362 2.027385 CAAGATTCCCTTAGGCTTGCC 58.973 52.381 2.97 2.97 32.86 4.52
3657 5364 2.027385 GGCAAGATTCCCTTAGGCTTG 58.973 52.381 10.63 10.63 39.06 4.01
3658 5365 1.640670 TGGCAAGATTCCCTTAGGCTT 59.359 47.619 0.00 0.00 32.86 4.35
3659 5366 1.064389 GTGGCAAGATTCCCTTAGGCT 60.064 52.381 0.00 0.00 32.86 4.58
3660 5367 1.340991 TGTGGCAAGATTCCCTTAGGC 60.341 52.381 0.00 0.00 32.86 3.93
3661 5368 2.025887 AGTGTGGCAAGATTCCCTTAGG 60.026 50.000 0.00 0.00 32.86 2.69
3662 5369 3.356529 AGTGTGGCAAGATTCCCTTAG 57.643 47.619 0.00 0.00 32.86 2.18
3663 5370 3.806949 AAGTGTGGCAAGATTCCCTTA 57.193 42.857 0.00 0.00 32.86 2.69
3664 5371 2.683211 AAGTGTGGCAAGATTCCCTT 57.317 45.000 0.00 0.00 34.91 3.95
3665 5372 2.683211 AAAGTGTGGCAAGATTCCCT 57.317 45.000 0.00 0.00 0.00 4.20
3666 5373 3.181466 ACAAAAAGTGTGGCAAGATTCCC 60.181 43.478 0.00 0.00 39.72 3.97
3667 5374 4.058721 ACAAAAAGTGTGGCAAGATTCC 57.941 40.909 0.00 0.00 39.72 3.01
3680 5387 4.501229 CCACATGGCATACACACAAAAAGT 60.501 41.667 0.00 0.00 0.00 2.66
3681 5388 3.989167 CCACATGGCATACACACAAAAAG 59.011 43.478 0.00 0.00 0.00 2.27
3682 5389 3.244009 CCCACATGGCATACACACAAAAA 60.244 43.478 0.00 0.00 0.00 1.94
3683 5390 2.298446 CCCACATGGCATACACACAAAA 59.702 45.455 0.00 0.00 0.00 2.44
3684 5391 1.891811 CCCACATGGCATACACACAAA 59.108 47.619 0.00 0.00 0.00 2.83
3685 5392 1.543607 CCCACATGGCATACACACAA 58.456 50.000 0.00 0.00 0.00 3.33
3686 5393 0.323269 CCCCACATGGCATACACACA 60.323 55.000 0.00 0.00 0.00 3.72
3687 5394 2.492418 CCCCACATGGCATACACAC 58.508 57.895 0.00 0.00 0.00 3.82
3696 5403 2.681064 CACTTGGGCCCCACATGG 60.681 66.667 22.27 5.25 30.78 3.66
3697 5404 2.118076 ACACTTGGGCCCCACATG 59.882 61.111 22.27 14.99 30.78 3.21
3698 5405 2.118076 CACACTTGGGCCCCACAT 59.882 61.111 22.27 0.00 30.78 3.21
3699 5406 4.217210 CCACACTTGGGCCCCACA 62.217 66.667 22.27 1.50 39.57 4.17
3709 5416 2.094234 GTGTTTGGTTCAAGCCACACTT 60.094 45.455 10.53 0.00 39.31 3.16
3710 5417 1.476488 GTGTTTGGTTCAAGCCACACT 59.524 47.619 10.53 0.00 39.31 3.55
3711 5418 1.476488 AGTGTTTGGTTCAAGCCACAC 59.524 47.619 10.00 10.00 39.10 3.82
3712 5419 1.748493 GAGTGTTTGGTTCAAGCCACA 59.252 47.619 11.95 0.00 38.42 4.17
3713 5420 1.748493 TGAGTGTTTGGTTCAAGCCAC 59.252 47.619 0.00 0.00 38.42 5.01
3714 5421 1.748493 GTGAGTGTTTGGTTCAAGCCA 59.252 47.619 0.00 0.00 36.62 4.75
3715 5422 1.067060 GGTGAGTGTTTGGTTCAAGCC 59.933 52.381 0.00 0.00 0.00 4.35
3716 5423 2.024414 AGGTGAGTGTTTGGTTCAAGC 58.976 47.619 0.00 0.00 0.00 4.01
3717 5424 4.881850 ACTTAGGTGAGTGTTTGGTTCAAG 59.118 41.667 0.00 0.00 0.00 3.02
3718 5425 4.850680 ACTTAGGTGAGTGTTTGGTTCAA 58.149 39.130 0.00 0.00 0.00 2.69
3719 5426 4.497291 ACTTAGGTGAGTGTTTGGTTCA 57.503 40.909 0.00 0.00 0.00 3.18
3720 5427 4.879545 TCAACTTAGGTGAGTGTTTGGTTC 59.120 41.667 0.00 0.00 0.00 3.62
3721 5428 4.850680 TCAACTTAGGTGAGTGTTTGGTT 58.149 39.130 0.00 0.00 0.00 3.67
3722 5429 4.497291 TCAACTTAGGTGAGTGTTTGGT 57.503 40.909 0.00 0.00 0.00 3.67
3723 5430 5.063204 TGATCAACTTAGGTGAGTGTTTGG 58.937 41.667 6.05 0.00 0.00 3.28
3724 5431 6.618287 TTGATCAACTTAGGTGAGTGTTTG 57.382 37.500 6.05 0.00 0.00 2.93
3725 5432 6.828785 AGTTTGATCAACTTAGGTGAGTGTTT 59.171 34.615 7.89 0.00 43.89 2.83
3726 5433 6.357367 AGTTTGATCAACTTAGGTGAGTGTT 58.643 36.000 7.89 0.00 43.89 3.32
3727 5434 5.930135 AGTTTGATCAACTTAGGTGAGTGT 58.070 37.500 7.89 0.00 43.89 3.55
3754 5461 7.584987 CCAAAGATTGTCACACCTAAACTTAG 58.415 38.462 0.00 0.00 0.00 2.18
3755 5462 6.016610 GCCAAAGATTGTCACACCTAAACTTA 60.017 38.462 0.00 0.00 0.00 2.24
3756 5463 5.221244 GCCAAAGATTGTCACACCTAAACTT 60.221 40.000 0.00 0.00 0.00 2.66
3757 5464 4.278419 GCCAAAGATTGTCACACCTAAACT 59.722 41.667 0.00 0.00 0.00 2.66
3758 5465 4.037446 TGCCAAAGATTGTCACACCTAAAC 59.963 41.667 0.00 0.00 0.00 2.01
3759 5466 4.211125 TGCCAAAGATTGTCACACCTAAA 58.789 39.130 0.00 0.00 0.00 1.85
3760 5467 3.826524 TGCCAAAGATTGTCACACCTAA 58.173 40.909 0.00 0.00 0.00 2.69
3761 5468 3.500448 TGCCAAAGATTGTCACACCTA 57.500 42.857 0.00 0.00 0.00 3.08
3762 5469 2.363306 TGCCAAAGATTGTCACACCT 57.637 45.000 0.00 0.00 0.00 4.00
3763 5470 3.181476 ACTTTGCCAAAGATTGTCACACC 60.181 43.478 23.32 0.00 41.02 4.16
3764 5471 4.045636 ACTTTGCCAAAGATTGTCACAC 57.954 40.909 23.32 0.00 41.02 3.82
3765 5472 4.734398 AACTTTGCCAAAGATTGTCACA 57.266 36.364 23.32 0.00 41.02 3.58
3766 5473 5.831997 ACTAACTTTGCCAAAGATTGTCAC 58.168 37.500 23.32 0.00 41.02 3.67
3767 5474 5.592282 TGACTAACTTTGCCAAAGATTGTCA 59.408 36.000 27.49 27.49 45.69 3.58
3768 5475 5.915196 GTGACTAACTTTGCCAAAGATTGTC 59.085 40.000 24.34 24.34 42.13 3.18
3769 5476 5.359576 TGTGACTAACTTTGCCAAAGATTGT 59.640 36.000 23.32 17.56 41.02 2.71
3770 5477 5.830912 TGTGACTAACTTTGCCAAAGATTG 58.169 37.500 23.32 14.58 41.02 2.67
3771 5478 6.463995 TTGTGACTAACTTTGCCAAAGATT 57.536 33.333 23.32 14.98 41.02 2.40
3772 5479 6.273071 GTTTGTGACTAACTTTGCCAAAGAT 58.727 36.000 23.32 14.26 41.02 2.40
3773 5480 5.393678 GGTTTGTGACTAACTTTGCCAAAGA 60.394 40.000 23.32 1.30 41.02 2.52
3774 5481 4.803613 GGTTTGTGACTAACTTTGCCAAAG 59.196 41.667 15.47 15.47 44.10 2.77
3775 5482 4.220821 TGGTTTGTGACTAACTTTGCCAAA 59.779 37.500 9.55 0.00 0.00 3.28
3776 5483 3.764434 TGGTTTGTGACTAACTTTGCCAA 59.236 39.130 9.55 0.00 0.00 4.52
3777 5484 3.357203 TGGTTTGTGACTAACTTTGCCA 58.643 40.909 9.55 0.00 0.00 4.92
3778 5485 4.379339 TTGGTTTGTGACTAACTTTGCC 57.621 40.909 9.55 0.00 0.00 4.52
3779 5486 5.164954 TGTTTGGTTTGTGACTAACTTTGC 58.835 37.500 9.55 0.62 0.00 3.68
3780 5487 5.288472 GCTGTTTGGTTTGTGACTAACTTTG 59.712 40.000 9.55 0.00 0.00 2.77
3781 5488 5.407502 GCTGTTTGGTTTGTGACTAACTTT 58.592 37.500 9.55 0.00 0.00 2.66
3782 5489 4.142249 GGCTGTTTGGTTTGTGACTAACTT 60.142 41.667 9.55 0.00 0.00 2.66
3783 5490 3.380320 GGCTGTTTGGTTTGTGACTAACT 59.620 43.478 9.55 0.00 0.00 2.24
3784 5491 3.490249 GGGCTGTTTGGTTTGTGACTAAC 60.490 47.826 1.25 1.25 0.00 2.34
3785 5492 2.691011 GGGCTGTTTGGTTTGTGACTAA 59.309 45.455 0.00 0.00 0.00 2.24
3786 5493 2.303175 GGGCTGTTTGGTTTGTGACTA 58.697 47.619 0.00 0.00 0.00 2.59
3787 5494 1.111277 GGGCTGTTTGGTTTGTGACT 58.889 50.000 0.00 0.00 0.00 3.41
3788 5495 0.104120 GGGGCTGTTTGGTTTGTGAC 59.896 55.000 0.00 0.00 0.00 3.67
3789 5496 0.032615 AGGGGCTGTTTGGTTTGTGA 60.033 50.000 0.00 0.00 0.00 3.58
3790 5497 0.829990 AAGGGGCTGTTTGGTTTGTG 59.170 50.000 0.00 0.00 0.00 3.33
3791 5498 2.316108 CTAAGGGGCTGTTTGGTTTGT 58.684 47.619 0.00 0.00 0.00 2.83
3792 5499 2.316108 ACTAAGGGGCTGTTTGGTTTG 58.684 47.619 0.00 0.00 0.00 2.93
3793 5500 2.767644 ACTAAGGGGCTGTTTGGTTT 57.232 45.000 0.00 0.00 0.00 3.27
3794 5501 4.397919 AATACTAAGGGGCTGTTTGGTT 57.602 40.909 0.00 0.00 0.00 3.67
3795 5502 4.202631 TGAAATACTAAGGGGCTGTTTGGT 60.203 41.667 0.00 0.00 0.00 3.67
3796 5503 4.157840 GTGAAATACTAAGGGGCTGTTTGG 59.842 45.833 0.00 0.00 0.00 3.28
3797 5504 4.764823 TGTGAAATACTAAGGGGCTGTTTG 59.235 41.667 0.00 0.00 0.00 2.93
3798 5505 4.993028 TGTGAAATACTAAGGGGCTGTTT 58.007 39.130 0.00 0.00 0.00 2.83
3799 5506 4.650972 TGTGAAATACTAAGGGGCTGTT 57.349 40.909 0.00 0.00 0.00 3.16
3800 5507 4.862641 ATGTGAAATACTAAGGGGCTGT 57.137 40.909 0.00 0.00 0.00 4.40
3801 5508 6.595716 GCTATATGTGAAATACTAAGGGGCTG 59.404 42.308 0.00 0.00 0.00 4.85
3802 5509 6.502158 AGCTATATGTGAAATACTAAGGGGCT 59.498 38.462 0.00 0.00 0.00 5.19
3803 5510 6.595716 CAGCTATATGTGAAATACTAAGGGGC 59.404 42.308 0.00 0.00 0.00 5.80
3804 5511 7.106239 CCAGCTATATGTGAAATACTAAGGGG 58.894 42.308 0.00 0.00 0.00 4.79
3805 5512 6.595716 GCCAGCTATATGTGAAATACTAAGGG 59.404 42.308 0.00 0.00 0.00 3.95
3806 5513 7.161404 TGCCAGCTATATGTGAAATACTAAGG 58.839 38.462 0.00 0.00 0.00 2.69
3807 5514 7.332926 CCTGCCAGCTATATGTGAAATACTAAG 59.667 40.741 0.00 0.00 0.00 2.18
3923 5630 7.373778 ACTTACCGACAATCAATAAAAGGTC 57.626 36.000 0.00 0.00 32.47 3.85
4141 5848 6.969993 TTGTTGCTTTAACCCACTAATCTT 57.030 33.333 0.00 0.00 38.55 2.40
4201 5908 9.542462 GATAGTAACACTTATGATGCTGGTTTA 57.458 33.333 0.00 0.00 0.00 2.01
4357 6064 9.548208 GAGATCAACTTAAAACAAAGTAGATGC 57.452 33.333 0.00 0.00 38.76 3.91
4497 6204 1.754226 CTAGCCTCTTCCTGTCTCCAC 59.246 57.143 0.00 0.00 0.00 4.02
4814 6521 3.846405 AAGTCGAGGTCCAGGGCCA 62.846 63.158 14.32 0.00 0.00 5.36
5244 7224 2.238521 AGGGGTTAGCAACACACAATG 58.761 47.619 4.13 0.00 36.19 2.82
5245 7225 2.675658 AGGGGTTAGCAACACACAAT 57.324 45.000 4.13 0.00 36.19 2.71
5246 7226 2.445682 AAGGGGTTAGCAACACACAA 57.554 45.000 4.13 0.00 36.19 3.33
5247 7227 2.445682 AAAGGGGTTAGCAACACACA 57.554 45.000 4.13 0.00 36.19 3.72
5248 7228 2.956333 AGAAAAGGGGTTAGCAACACAC 59.044 45.455 4.13 0.00 36.19 3.82
5249 7229 2.955660 CAGAAAAGGGGTTAGCAACACA 59.044 45.455 4.13 0.00 36.19 3.72
5250 7230 3.219281 TCAGAAAAGGGGTTAGCAACAC 58.781 45.455 0.00 0.00 0.00 3.32
5251 7231 3.586470 TCAGAAAAGGGGTTAGCAACA 57.414 42.857 0.00 0.00 0.00 3.33
5378 7368 3.958860 AGCTGACAGGGGCCACAC 61.959 66.667 8.31 0.00 0.00 3.82
5450 7440 3.099141 AGCAAAGAATACCCATGGTTGG 58.901 45.455 11.73 0.00 43.23 3.77
5453 7443 2.311542 TCCAGCAAAGAATACCCATGGT 59.688 45.455 11.73 1.30 40.16 3.55
5468 7458 2.357637 CGAAAAGGAAACAACTCCAGCA 59.642 45.455 0.00 0.00 38.02 4.41
5497 7487 1.227205 CAGGCAAGCACCGCAAAAA 60.227 52.632 0.00 0.00 33.69 1.94
5498 7488 2.416678 CAGGCAAGCACCGCAAAA 59.583 55.556 0.00 0.00 33.69 2.44
5499 7489 3.604667 CCAGGCAAGCACCGCAAA 61.605 61.111 0.00 0.00 33.69 3.68
5526 7516 2.435762 TGCATTCCGCGCTTGCTA 60.436 55.556 21.24 9.61 46.97 3.49
5540 7530 2.758327 AGTCGGGGCTATCGTGCA 60.758 61.111 0.00 0.00 34.04 4.57
5547 7537 2.764737 ATCGGAGGAGTCGGGGCTA 61.765 63.158 0.00 0.00 0.00 3.93
5608 7598 1.869767 CCGACTGCATTGAGCTAATCC 59.130 52.381 0.00 0.00 45.94 3.01
5616 7606 0.894835 TGTAGAGCCGACTGCATTGA 59.105 50.000 0.00 0.00 44.83 2.57
5624 7614 0.680280 TCTCCAGGTGTAGAGCCGAC 60.680 60.000 0.00 0.00 0.00 4.79
5636 7626 2.376063 TGGTGTGACCATCTCCAGG 58.624 57.895 0.00 0.00 44.79 4.45
5645 7635 1.258445 ACTCTCCCGATGGTGTGACC 61.258 60.000 0.00 0.00 39.22 4.02
5646 7636 1.134560 GTACTCTCCCGATGGTGTGAC 59.865 57.143 0.00 0.00 0.00 3.67
5647 7637 1.471119 GTACTCTCCCGATGGTGTGA 58.529 55.000 0.00 0.00 0.00 3.58
5648 7638 0.100682 CGTACTCTCCCGATGGTGTG 59.899 60.000 0.00 0.00 0.00 3.82
5649 7639 1.664321 GCGTACTCTCCCGATGGTGT 61.664 60.000 0.00 0.00 0.00 4.16
5653 7643 1.299468 GCAGCGTACTCTCCCGATG 60.299 63.158 0.00 0.00 42.84 3.84
5654 7644 2.835705 CGCAGCGTACTCTCCCGAT 61.836 63.158 6.65 0.00 0.00 4.18
5656 7646 3.456431 CTCGCAGCGTACTCTCCCG 62.456 68.421 15.93 0.00 0.00 5.14
5658 7648 2.278271 GCTCGCAGCGTACTCTCC 60.278 66.667 15.93 0.00 0.00 3.71
5668 7658 2.505777 CCGTGACTGAGCTCGCAG 60.506 66.667 9.64 4.96 41.63 5.18
5669 7659 4.724602 GCCGTGACTGAGCTCGCA 62.725 66.667 9.64 4.39 0.00 5.10
5678 7672 4.694233 CAGCTGCAGGCCGTGACT 62.694 66.667 17.12 0.00 43.05 3.41
5725 7719 2.781300 GCTACACGCTGCTTGAGC 59.219 61.111 13.42 12.65 45.20 4.26
5735 7729 1.132643 AGTTTCTCTAGCCGCTACACG 59.867 52.381 0.00 0.00 43.15 4.49
5760 7754 0.746659 GCAACCAGTCAAGGTGCTTT 59.253 50.000 0.00 0.00 42.25 3.51
5763 7757 1.656441 CTGCAACCAGTCAAGGTGC 59.344 57.895 0.00 0.00 42.25 5.01
5765 7759 0.466189 CACCTGCAACCAGTCAAGGT 60.466 55.000 0.00 0.00 45.91 3.50
5788 7782 1.006571 TTGTCGTCGGACCTGAAGC 60.007 57.895 1.91 0.00 42.73 3.86
5795 7789 1.337821 GATGTCACTTGTCGTCGGAC 58.662 55.000 0.00 0.00 43.71 4.79
5838 7842 3.866327 GCACTTTTTAACCCGCTTTGAAA 59.134 39.130 0.00 0.00 0.00 2.69
5841 7845 3.092334 AGCACTTTTTAACCCGCTTTG 57.908 42.857 0.00 0.00 0.00 2.77
5866 7875 2.413112 GTGAGATGACAATGACCACGTG 59.587 50.000 9.08 9.08 0.00 4.49
5867 7876 2.688507 GTGAGATGACAATGACCACGT 58.311 47.619 0.00 0.00 0.00 4.49
5870 7879 3.006859 ACTTCGTGAGATGACAATGACCA 59.993 43.478 0.00 0.00 41.60 4.02
5877 7886 5.897377 TTCATAGACTTCGTGAGATGACA 57.103 39.130 0.00 0.00 41.60 3.58
5889 7898 4.143179 GCGTTACGTTGCTTTCATAGACTT 60.143 41.667 6.63 0.00 0.00 3.01
5891 7900 3.122278 TGCGTTACGTTGCTTTCATAGAC 59.878 43.478 6.63 0.00 0.00 2.59
5906 7915 1.873698 TGAGAACACCCTTGCGTTAC 58.126 50.000 0.00 0.00 0.00 2.50
5907 7916 2.623878 TTGAGAACACCCTTGCGTTA 57.376 45.000 0.00 0.00 0.00 3.18
5911 7920 2.229784 CTCCATTTGAGAACACCCTTGC 59.770 50.000 0.00 0.00 44.42 4.01
5981 7990 1.194781 GGCACTCCTCCAAGTCCTCA 61.195 60.000 0.00 0.00 0.00 3.86
5985 7994 2.266055 CCGGCACTCCTCCAAGTC 59.734 66.667 0.00 0.00 0.00 3.01
6000 8009 2.159421 ACTATCTAGACGCACAACACCG 60.159 50.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.