Multiple sequence alignment - TraesCS6D01G180100

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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 TraesCS6D01G180100 chr6D 100.000 3601 0 0 1 3601 198604325 198600725 0.000000e+00 6650.0
1 TraesCS6D01G180100 chr6A 95.417 2531 72 19 783 3289 299717125 299719635 0.000000e+00 3991.0
2 TraesCS6D01G180100 chr6A 92.583 782 56 2 1 781 299716184 299716964 0.000000e+00 1122.0
3 TraesCS6D01G180100 chr6A 92.523 107 8 0 1 107 418651199 418651305 1.730000e-33 154.0
4 TraesCS6D01G180100 chr6B 94.995 2058 82 9 821 2862 371610190 371612242 0.000000e+00 3210.0
5 TraesCS6D01G180100 chr6B 91.560 782 60 6 1 778 371600795 371601574 0.000000e+00 1074.0
6 TraesCS6D01G180100 chr6B 92.844 559 40 0 105 663 522330068 522330626 0.000000e+00 811.0
7 TraesCS6D01G180100 chr6B 82.460 439 72 5 2170 2604 347119912 347119475 2.620000e-101 379.0
8 TraesCS6D01G180100 chr6B 85.197 304 21 7 2781 3076 371612319 371612606 1.260000e-74 291.0
9 TraesCS6D01G180100 chr6B 100.000 30 0 0 3115 3144 371612659 371612688 5.020000e-04 56.5
10 TraesCS6D01G180100 chr6B 100.000 29 0 0 3088 3116 371612603 371612631 2.000000e-03 54.7
11 TraesCS6D01G180100 chr5A 93.202 559 38 0 105 663 257362303 257362861 0.000000e+00 822.0
12 TraesCS6D01G180100 chr5A 93.036 560 39 0 105 664 82312697 82313256 0.000000e+00 819.0
13 TraesCS6D01G180100 chr5A 89.655 116 10 2 664 778 520646049 520646163 2.900000e-31 147.0
14 TraesCS6D01G180100 chr5A 87.387 111 13 1 1 111 284967430 284967539 3.770000e-25 126.0
15 TraesCS6D01G180100 chr7B 93.048 561 39 0 105 665 443304634 443304074 0.000000e+00 821.0
16 TraesCS6D01G180100 chr7B 92.844 559 40 0 105 663 396641693 396641135 0.000000e+00 811.0
17 TraesCS6D01G180100 chr7B 96.629 89 3 0 4 92 474136314 474136226 8.060000e-32 148.0
18 TraesCS6D01G180100 chr2A 91.624 585 48 1 105 688 440267431 440266847 0.000000e+00 808.0
19 TraesCS6D01G180100 chr1A 91.738 581 46 2 105 685 491265246 491264668 0.000000e+00 806.0
20 TraesCS6D01G180100 chr7D 82.578 287 44 6 3189 3471 110791050 110791334 7.720000e-62 248.0
21 TraesCS6D01G180100 chr4B 88.889 117 11 1 664 778 40229454 40229570 3.750000e-30 143.0
22 TraesCS6D01G180100 chr4B 96.970 33 1 0 746 778 546659998 546659966 5.020000e-04 56.5
23 TraesCS6D01G180100 chr7A 88.393 112 13 0 1 112 376320677 376320788 6.270000e-28 135.0
24 TraesCS6D01G180100 chr7A 91.837 49 3 1 737 784 427620922 427620874 2.320000e-07 67.6
25 TraesCS6D01G180100 chr3D 90.196 102 10 0 7 108 178367894 178367793 2.260000e-27 134.0
26 TraesCS6D01G180100 chr4D 88.785 107 12 0 1 107 139480779 139480885 8.110000e-27 132.0
27 TraesCS6D01G180100 chr4D 88.785 107 12 0 1 107 362326479 362326585 8.110000e-27 132.0
28 TraesCS6D01G180100 chr3B 92.500 40 2 1 750 788 136335449 136335410 5.020000e-04 56.5


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 TraesCS6D01G180100 chr6D 198600725 198604325 3600 True 6650.00 6650 100.000 1 3601 1 chr6D.!!$R1 3600
1 TraesCS6D01G180100 chr6A 299716184 299719635 3451 False 2556.50 3991 94.000 1 3289 2 chr6A.!!$F2 3288
2 TraesCS6D01G180100 chr6B 371600795 371601574 779 False 1074.00 1074 91.560 1 778 1 chr6B.!!$F1 777
3 TraesCS6D01G180100 chr6B 371610190 371612688 2498 False 903.05 3210 95.048 821 3144 4 chr6B.!!$F3 2323
4 TraesCS6D01G180100 chr6B 522330068 522330626 558 False 811.00 811 92.844 105 663 1 chr6B.!!$F2 558
5 TraesCS6D01G180100 chr5A 257362303 257362861 558 False 822.00 822 93.202 105 663 1 chr5A.!!$F2 558
6 TraesCS6D01G180100 chr5A 82312697 82313256 559 False 819.00 819 93.036 105 664 1 chr5A.!!$F1 559
7 TraesCS6D01G180100 chr7B 443304074 443304634 560 True 821.00 821 93.048 105 665 1 chr7B.!!$R2 560
8 TraesCS6D01G180100 chr7B 396641135 396641693 558 True 811.00 811 92.844 105 663 1 chr7B.!!$R1 558
9 TraesCS6D01G180100 chr2A 440266847 440267431 584 True 808.00 808 91.624 105 688 1 chr2A.!!$R1 583
10 TraesCS6D01G180100 chr1A 491264668 491265246 578 True 806.00 806 91.738 105 685 1 chr1A.!!$R1 580

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
628 632 1.766496 CTCATCCTTTACCCCGGCTTA 59.234 52.381 0.0 0.0 0.0 3.09 F
836 1001 2.162120 TACGCATAACAGCACGCCG 61.162 57.895 0.0 0.0 0.0 6.46 F
1488 1661 0.944311 CGTTGCTTCGTGTGCTAGGT 60.944 55.000 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1609 1.333636 ATGAGGAGAAGGCCGGACTG 61.334 60.0 12.91 0.0 0.00 3.51 R
2495 2676 2.299993 TAGCCTTGATCAACTCAGCG 57.700 50.0 3.38 0.0 34.68 5.18 R
3377 3765 0.106521 TCTAGCAGCACACACAAGCA 59.893 50.0 0.00 0.0 0.00 3.91 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
25 26 5.975693 TGGATTGATAACCTTGGTTTCAC 57.024 39.130 10.52 3.90 0.00 3.18
55 56 4.323562 GGGAAATACTTACCTCTGCTGTGT 60.324 45.833 0.00 0.00 31.91 3.72
67 68 4.100035 CCTCTGCTGTGTTGTATCATCCTA 59.900 45.833 0.00 0.00 0.00 2.94
75 76 7.437713 TGTGTTGTATCATCCTATCCTCTTT 57.562 36.000 0.00 0.00 0.00 2.52
98 99 2.616842 GGGAAATACCAACGCGAATCAT 59.383 45.455 15.93 0.00 41.20 2.45
242 243 2.897969 TCAACTAACTCCCGAAGCTTCT 59.102 45.455 23.50 6.87 0.00 2.85
421 423 2.842394 ATCCTCGCTCACTTGCCACG 62.842 60.000 0.00 0.00 0.00 4.94
542 546 3.603158 GGTTATGCCCCAACGAATTTT 57.397 42.857 0.00 0.00 0.00 1.82
603 607 4.040068 GCTCGCCAAGCCTATGAG 57.960 61.111 0.00 0.00 45.92 2.90
622 626 2.172930 GAGAACCCTCATCCTTTACCCC 59.827 54.545 0.00 0.00 39.24 4.95
628 632 1.766496 CTCATCCTTTACCCCGGCTTA 59.234 52.381 0.00 0.00 0.00 3.09
781 787 6.052840 GCACGTGCATACTAACTAGTACTA 57.947 41.667 34.52 1.89 41.18 1.82
836 1001 2.162120 TACGCATAACAGCACGCCG 61.162 57.895 0.00 0.00 0.00 6.46
1436 1609 0.957888 GGTGTTCCTCAAGCAGCTCC 60.958 60.000 0.00 0.00 0.00 4.70
1464 1637 2.102252 GCCTTCTCCTCATCACTGGTAG 59.898 54.545 0.00 0.00 0.00 3.18
1488 1661 0.944311 CGTTGCTTCGTGTGCTAGGT 60.944 55.000 0.00 0.00 0.00 3.08
1773 1950 9.385902 CAGTGTGTTTAGTAATGTGATTTTGAG 57.614 33.333 0.00 0.00 0.00 3.02
1832 2009 4.023193 AGTGTTTTGTAAATGCCCTCGAAG 60.023 41.667 0.00 0.00 0.00 3.79
1966 2145 1.337118 TTGTTGGCAGTCCCATTTCC 58.663 50.000 0.00 0.00 44.89 3.13
2022 2201 7.440556 ACTTAGATTCATGATTCGGATGACTTG 59.559 37.037 11.02 0.00 29.39 3.16
2071 2250 3.821033 AGTGGGAGTTGTTTGCTGATAAC 59.179 43.478 0.00 0.00 0.00 1.89
2118 2299 6.299141 TCTTTATTCTCAAGCACTGGACTTT 58.701 36.000 0.00 0.00 0.00 2.66
2294 2475 6.017934 TGCAGAAGTTTGATGACAAGTACTTC 60.018 38.462 4.77 14.39 44.99 3.01
2351 2532 1.269831 GGCGAGCTATTTGAGTCGGAT 60.270 52.381 0.00 0.00 32.60 4.18
2498 2679 3.540211 CCAGAAGGTCATTGACGCT 57.460 52.632 10.56 6.38 32.65 5.07
2777 2958 0.829990 CCCCTTTGTTGGCTTGTTGT 59.170 50.000 0.00 0.00 0.00 3.32
2794 3055 6.462552 TTGTTGTGACATTTTCTTGATCCA 57.537 33.333 0.00 0.00 35.29 3.41
2912 3253 8.807948 AATTTGCAAGTAGGTCAACAGTATAT 57.192 30.769 0.00 0.00 0.00 0.86
2944 3285 0.535780 TTGCAGAGCTTGGACAGTGG 60.536 55.000 0.00 0.00 0.00 4.00
3046 3392 3.915346 ATGGTTTAGGGAAAGTTGGGT 57.085 42.857 0.00 0.00 0.00 4.51
3076 3425 7.608308 AAGAGCAACAGATCTTGTAATCTTC 57.392 36.000 0.00 0.00 39.73 2.87
3077 3426 6.945218 AGAGCAACAGATCTTGTAATCTTCT 58.055 36.000 0.00 0.00 39.73 2.85
3079 3428 7.882271 AGAGCAACAGATCTTGTAATCTTCTTT 59.118 33.333 0.00 0.00 39.73 2.52
3080 3429 7.814642 AGCAACAGATCTTGTAATCTTCTTTG 58.185 34.615 0.00 0.00 39.73 2.77
3081 3430 7.663081 AGCAACAGATCTTGTAATCTTCTTTGA 59.337 33.333 0.00 0.00 39.73 2.69
3083 3432 9.604626 CAACAGATCTTGTAATCTTCTTTGAAC 57.395 33.333 0.00 0.00 39.73 3.18
3084 3433 8.023050 ACAGATCTTGTAATCTTCTTTGAACG 57.977 34.615 0.00 0.00 38.56 3.95
3209 3597 3.164268 TGTTGGCACTTATGGAAGCATT 58.836 40.909 0.00 0.00 35.97 3.56
3231 3619 4.263435 TGTAACGGATTGGTATTTGGACC 58.737 43.478 0.00 0.00 40.21 4.46
3262 3650 1.630369 AGCTTGACAGTGCCCATCTTA 59.370 47.619 0.00 0.00 0.00 2.10
3289 3677 4.081198 AGTCAGGTCTTTGATGAGCTTAGG 60.081 45.833 0.00 0.00 42.10 2.69
3290 3678 3.840666 TCAGGTCTTTGATGAGCTTAGGT 59.159 43.478 0.00 0.00 42.10 3.08
3291 3679 4.081420 TCAGGTCTTTGATGAGCTTAGGTC 60.081 45.833 4.26 4.26 42.10 3.85
3292 3680 3.198853 AGGTCTTTGATGAGCTTAGGTCC 59.801 47.826 9.04 0.00 41.36 4.46
3293 3681 3.198853 GGTCTTTGATGAGCTTAGGTCCT 59.801 47.826 9.04 0.00 0.00 3.85
3294 3682 4.187694 GTCTTTGATGAGCTTAGGTCCTG 58.812 47.826 9.04 0.00 0.00 3.86
3295 3683 3.198635 TCTTTGATGAGCTTAGGTCCTGG 59.801 47.826 9.04 0.00 0.00 4.45
3296 3684 1.500474 TGATGAGCTTAGGTCCTGGG 58.500 55.000 9.04 0.00 0.00 4.45
3297 3685 1.273838 TGATGAGCTTAGGTCCTGGGT 60.274 52.381 9.04 0.00 0.00 4.51
3298 3686 1.840635 GATGAGCTTAGGTCCTGGGTT 59.159 52.381 9.04 0.00 0.00 4.11
3299 3687 2.634639 TGAGCTTAGGTCCTGGGTTA 57.365 50.000 9.04 0.00 0.00 2.85
3300 3688 2.467880 TGAGCTTAGGTCCTGGGTTAG 58.532 52.381 9.04 0.00 0.00 2.34
3301 3689 2.043939 TGAGCTTAGGTCCTGGGTTAGA 59.956 50.000 9.04 0.00 0.00 2.10
3302 3690 2.696187 GAGCTTAGGTCCTGGGTTAGAG 59.304 54.545 0.00 0.00 0.00 2.43
3303 3691 1.139256 GCTTAGGTCCTGGGTTAGAGC 59.861 57.143 0.00 0.00 0.00 4.09
3304 3692 1.409427 CTTAGGTCCTGGGTTAGAGCG 59.591 57.143 0.00 0.00 35.67 5.03
3305 3693 0.396695 TAGGTCCTGGGTTAGAGCGG 60.397 60.000 0.00 0.00 35.67 5.52
3306 3694 2.732619 GGTCCTGGGTTAGAGCGGG 61.733 68.421 0.00 0.00 0.00 6.13
3307 3695 1.684734 GTCCTGGGTTAGAGCGGGA 60.685 63.158 0.00 0.00 0.00 5.14
3308 3696 1.381327 TCCTGGGTTAGAGCGGGAG 60.381 63.158 0.00 0.00 0.00 4.30
3321 3709 3.442996 CGGGAGCACAAGGAGTTAG 57.557 57.895 0.00 0.00 0.00 2.34
3322 3710 0.741221 CGGGAGCACAAGGAGTTAGC 60.741 60.000 0.00 0.00 0.00 3.09
3323 3711 0.324943 GGGAGCACAAGGAGTTAGCA 59.675 55.000 0.00 0.00 0.00 3.49
3324 3712 1.065126 GGGAGCACAAGGAGTTAGCAT 60.065 52.381 0.00 0.00 0.00 3.79
3325 3713 2.284190 GGAGCACAAGGAGTTAGCATC 58.716 52.381 0.00 0.00 0.00 3.91
3326 3714 2.093235 GGAGCACAAGGAGTTAGCATCT 60.093 50.000 0.00 0.00 0.00 2.90
3327 3715 3.604582 GAGCACAAGGAGTTAGCATCTT 58.395 45.455 0.00 0.00 0.00 2.40
3328 3716 4.006319 GAGCACAAGGAGTTAGCATCTTT 58.994 43.478 0.00 0.00 0.00 2.52
3329 3717 4.401925 AGCACAAGGAGTTAGCATCTTTT 58.598 39.130 0.00 0.00 0.00 2.27
3330 3718 4.217118 AGCACAAGGAGTTAGCATCTTTTG 59.783 41.667 0.00 0.00 0.00 2.44
3331 3719 4.022849 GCACAAGGAGTTAGCATCTTTTGT 60.023 41.667 0.00 0.00 0.00 2.83
3332 3720 5.455392 CACAAGGAGTTAGCATCTTTTGTG 58.545 41.667 13.51 13.51 36.06 3.33
3333 3721 5.239306 CACAAGGAGTTAGCATCTTTTGTGA 59.761 40.000 17.80 0.00 39.81 3.58
3334 3722 5.471456 ACAAGGAGTTAGCATCTTTTGTGAG 59.529 40.000 0.00 0.00 0.00 3.51
3335 3723 5.234466 AGGAGTTAGCATCTTTTGTGAGT 57.766 39.130 0.00 0.00 0.00 3.41
3336 3724 6.360370 AGGAGTTAGCATCTTTTGTGAGTA 57.640 37.500 0.00 0.00 0.00 2.59
3337 3725 6.402222 AGGAGTTAGCATCTTTTGTGAGTAG 58.598 40.000 0.00 0.00 0.00 2.57
3338 3726 6.014156 AGGAGTTAGCATCTTTTGTGAGTAGT 60.014 38.462 0.00 0.00 0.00 2.73
3339 3727 6.091441 GGAGTTAGCATCTTTTGTGAGTAGTG 59.909 42.308 0.00 0.00 0.00 2.74
3340 3728 5.934625 AGTTAGCATCTTTTGTGAGTAGTGG 59.065 40.000 0.00 0.00 0.00 4.00
3341 3729 4.357918 AGCATCTTTTGTGAGTAGTGGT 57.642 40.909 0.00 0.00 0.00 4.16
3342 3730 4.319177 AGCATCTTTTGTGAGTAGTGGTC 58.681 43.478 0.00 0.00 0.00 4.02
3343 3731 3.123621 GCATCTTTTGTGAGTAGTGGTCG 59.876 47.826 0.00 0.00 0.00 4.79
3344 3732 4.307432 CATCTTTTGTGAGTAGTGGTCGT 58.693 43.478 0.00 0.00 0.00 4.34
3345 3733 3.713288 TCTTTTGTGAGTAGTGGTCGTG 58.287 45.455 0.00 0.00 0.00 4.35
3346 3734 3.131577 TCTTTTGTGAGTAGTGGTCGTGT 59.868 43.478 0.00 0.00 0.00 4.49
3347 3735 4.338964 TCTTTTGTGAGTAGTGGTCGTGTA 59.661 41.667 0.00 0.00 0.00 2.90
3348 3736 3.909776 TTGTGAGTAGTGGTCGTGTAG 57.090 47.619 0.00 0.00 0.00 2.74
3349 3737 2.854963 TGTGAGTAGTGGTCGTGTAGT 58.145 47.619 0.00 0.00 0.00 2.73
3350 3738 4.006780 TGTGAGTAGTGGTCGTGTAGTA 57.993 45.455 0.00 0.00 0.00 1.82
3351 3739 3.999001 TGTGAGTAGTGGTCGTGTAGTAG 59.001 47.826 0.00 0.00 0.00 2.57
3352 3740 3.373439 GTGAGTAGTGGTCGTGTAGTAGG 59.627 52.174 0.00 0.00 0.00 3.18
3353 3741 3.261643 TGAGTAGTGGTCGTGTAGTAGGA 59.738 47.826 0.00 0.00 0.00 2.94
3354 3742 3.870419 GAGTAGTGGTCGTGTAGTAGGAG 59.130 52.174 0.00 0.00 0.00 3.69
3355 3743 2.875094 AGTGGTCGTGTAGTAGGAGT 57.125 50.000 0.00 0.00 0.00 3.85
3356 3744 2.434428 AGTGGTCGTGTAGTAGGAGTG 58.566 52.381 0.00 0.00 0.00 3.51
3357 3745 1.471684 GTGGTCGTGTAGTAGGAGTGG 59.528 57.143 0.00 0.00 0.00 4.00
3358 3746 1.352017 TGGTCGTGTAGTAGGAGTGGA 59.648 52.381 0.00 0.00 0.00 4.02
3359 3747 2.015587 GGTCGTGTAGTAGGAGTGGAG 58.984 57.143 0.00 0.00 0.00 3.86
3360 3748 2.015587 GTCGTGTAGTAGGAGTGGAGG 58.984 57.143 0.00 0.00 0.00 4.30
3361 3749 1.632409 TCGTGTAGTAGGAGTGGAGGT 59.368 52.381 0.00 0.00 0.00 3.85
3362 3750 2.840038 TCGTGTAGTAGGAGTGGAGGTA 59.160 50.000 0.00 0.00 0.00 3.08
3363 3751 3.118482 TCGTGTAGTAGGAGTGGAGGTAG 60.118 52.174 0.00 0.00 0.00 3.18
3364 3752 2.950975 GTGTAGTAGGAGTGGAGGTAGC 59.049 54.545 0.00 0.00 0.00 3.58
3365 3753 2.851194 TGTAGTAGGAGTGGAGGTAGCT 59.149 50.000 0.00 0.00 0.00 3.32
3366 3754 2.445682 AGTAGGAGTGGAGGTAGCTG 57.554 55.000 0.00 0.00 0.00 4.24
3367 3755 1.063567 AGTAGGAGTGGAGGTAGCTGG 60.064 57.143 0.00 0.00 0.00 4.85
3368 3756 0.261991 TAGGAGTGGAGGTAGCTGGG 59.738 60.000 0.00 0.00 0.00 4.45
3369 3757 2.736826 GGAGTGGAGGTAGCTGGGC 61.737 68.421 0.00 0.00 0.00 5.36
3370 3758 2.689034 AGTGGAGGTAGCTGGGCC 60.689 66.667 0.00 0.00 0.00 5.80
3371 3759 4.162690 GTGGAGGTAGCTGGGCCG 62.163 72.222 0.00 0.00 0.00 6.13
3386 3774 3.663176 CCGGCTGGTGCTTGTGTG 61.663 66.667 2.29 0.00 39.59 3.82
3387 3775 2.901840 CGGCTGGTGCTTGTGTGT 60.902 61.111 0.00 0.00 39.59 3.72
3388 3776 2.723746 GGCTGGTGCTTGTGTGTG 59.276 61.111 0.00 0.00 39.59 3.82
3389 3777 2.026590 GCTGGTGCTTGTGTGTGC 59.973 61.111 0.00 0.00 36.03 4.57
3390 3778 2.484062 GCTGGTGCTTGTGTGTGCT 61.484 57.895 0.00 0.00 36.03 4.40
3391 3779 1.357690 CTGGTGCTTGTGTGTGCTG 59.642 57.895 0.00 0.00 0.00 4.41
3392 3780 2.026590 GGTGCTTGTGTGTGCTGC 59.973 61.111 0.00 0.00 0.00 5.25
3393 3781 2.484062 GGTGCTTGTGTGTGCTGCT 61.484 57.895 0.00 0.00 0.00 4.24
3394 3782 1.165907 GGTGCTTGTGTGTGCTGCTA 61.166 55.000 0.00 0.00 0.00 3.49
3395 3783 0.236711 GTGCTTGTGTGTGCTGCTAG 59.763 55.000 0.00 0.00 0.00 3.42
3396 3784 0.106521 TGCTTGTGTGTGCTGCTAGA 59.893 50.000 0.00 0.00 0.00 2.43
3397 3785 0.795085 GCTTGTGTGTGCTGCTAGAG 59.205 55.000 0.00 0.00 0.00 2.43
3406 3794 3.776616 GCTGCTAGAGCCTTGATGT 57.223 52.632 0.00 0.00 42.54 3.06
3407 3795 2.898729 GCTGCTAGAGCCTTGATGTA 57.101 50.000 0.00 0.00 42.54 2.29
3408 3796 3.185246 GCTGCTAGAGCCTTGATGTAA 57.815 47.619 0.00 0.00 42.54 2.41
3409 3797 3.737850 GCTGCTAGAGCCTTGATGTAAT 58.262 45.455 0.00 0.00 42.54 1.89
3410 3798 3.745458 GCTGCTAGAGCCTTGATGTAATC 59.255 47.826 0.00 0.00 42.48 1.75
3411 3799 4.953667 CTGCTAGAGCCTTGATGTAATCA 58.046 43.478 0.00 0.00 46.60 2.57
3414 3802 6.959671 GCTAGAGCCTTGATGTAATCATAC 57.040 41.667 0.00 0.00 44.03 2.39
3415 3803 6.696411 GCTAGAGCCTTGATGTAATCATACT 58.304 40.000 0.00 0.00 44.03 2.12
3416 3804 6.811170 GCTAGAGCCTTGATGTAATCATACTC 59.189 42.308 0.00 0.03 44.03 2.59
3433 3821 8.839310 ATCATACTCTTGTACATATTTCTGCC 57.161 34.615 0.00 0.00 0.00 4.85
3434 3822 8.023021 TCATACTCTTGTACATATTTCTGCCT 57.977 34.615 0.00 0.00 0.00 4.75
3435 3823 8.144478 TCATACTCTTGTACATATTTCTGCCTC 58.856 37.037 0.00 0.00 0.00 4.70
3436 3824 5.675538 ACTCTTGTACATATTTCTGCCTCC 58.324 41.667 0.00 0.00 0.00 4.30
3437 3825 5.426833 ACTCTTGTACATATTTCTGCCTCCT 59.573 40.000 0.00 0.00 0.00 3.69
3438 3826 6.611642 ACTCTTGTACATATTTCTGCCTCCTA 59.388 38.462 0.00 0.00 0.00 2.94
3439 3827 7.291182 ACTCTTGTACATATTTCTGCCTCCTAT 59.709 37.037 0.00 0.00 0.00 2.57
3440 3828 8.721133 TCTTGTACATATTTCTGCCTCCTATA 57.279 34.615 0.00 0.00 0.00 1.31
3441 3829 9.154632 TCTTGTACATATTTCTGCCTCCTATAA 57.845 33.333 0.00 0.00 0.00 0.98
3442 3830 9.778741 CTTGTACATATTTCTGCCTCCTATAAA 57.221 33.333 0.00 0.00 0.00 1.40
3443 3831 9.778741 TTGTACATATTTCTGCCTCCTATAAAG 57.221 33.333 0.00 0.00 0.00 1.85
3444 3832 7.878127 TGTACATATTTCTGCCTCCTATAAAGC 59.122 37.037 0.00 0.00 0.00 3.51
3445 3833 6.241645 ACATATTTCTGCCTCCTATAAAGCC 58.758 40.000 0.00 0.00 0.00 4.35
3446 3834 4.796110 ATTTCTGCCTCCTATAAAGCCA 57.204 40.909 0.00 0.00 0.00 4.75
3447 3835 4.584638 TTTCTGCCTCCTATAAAGCCAA 57.415 40.909 0.00 0.00 0.00 4.52
3448 3836 3.845781 TCTGCCTCCTATAAAGCCAAG 57.154 47.619 0.00 0.00 0.00 3.61
3449 3837 2.439507 TCTGCCTCCTATAAAGCCAAGG 59.560 50.000 0.00 0.00 0.00 3.61
3450 3838 2.439507 CTGCCTCCTATAAAGCCAAGGA 59.560 50.000 0.00 0.00 37.07 3.36
3451 3839 2.849943 TGCCTCCTATAAAGCCAAGGAA 59.150 45.455 0.00 0.00 38.91 3.36
3452 3840 3.215151 GCCTCCTATAAAGCCAAGGAAC 58.785 50.000 0.00 0.00 38.91 3.62
3453 3841 3.467803 CCTCCTATAAAGCCAAGGAACG 58.532 50.000 0.00 0.00 38.91 3.95
3454 3842 2.872858 CTCCTATAAAGCCAAGGAACGC 59.127 50.000 0.00 0.00 38.91 4.84
3455 3843 1.597663 CCTATAAAGCCAAGGAACGCG 59.402 52.381 3.53 3.53 31.64 6.01
3456 3844 2.546778 CTATAAAGCCAAGGAACGCGA 58.453 47.619 15.93 0.00 0.00 5.87
3457 3845 2.038387 ATAAAGCCAAGGAACGCGAT 57.962 45.000 15.93 0.00 0.00 4.58
3458 3846 1.816074 TAAAGCCAAGGAACGCGATT 58.184 45.000 15.93 2.74 0.00 3.34
3459 3847 0.240945 AAAGCCAAGGAACGCGATTG 59.759 50.000 15.93 11.87 0.00 2.67
3460 3848 2.200170 AAGCCAAGGAACGCGATTGC 62.200 55.000 15.93 9.08 37.91 3.56
3473 3861 3.658351 GCGATTGCGTACTCTCAATTT 57.342 42.857 0.00 0.00 40.36 1.82
3474 3862 4.003519 GCGATTGCGTACTCTCAATTTT 57.996 40.909 0.00 0.00 40.36 1.82
3475 3863 4.403453 GCGATTGCGTACTCTCAATTTTT 58.597 39.130 0.00 0.00 40.36 1.94
3521 3909 3.678965 TTTTAAGGAGCCCATATGCCA 57.321 42.857 0.00 0.00 0.00 4.92
3522 3910 3.901570 TTTAAGGAGCCCATATGCCAT 57.098 42.857 0.00 0.00 0.00 4.40
3523 3911 3.439857 TTAAGGAGCCCATATGCCATC 57.560 47.619 0.00 0.00 0.00 3.51
3524 3912 1.453633 AAGGAGCCCATATGCCATCT 58.546 50.000 0.00 0.00 0.00 2.90
3525 3913 2.349167 AGGAGCCCATATGCCATCTA 57.651 50.000 0.00 0.00 0.00 1.98
3526 3914 2.194859 AGGAGCCCATATGCCATCTAG 58.805 52.381 0.00 0.00 0.00 2.43
3527 3915 1.211457 GGAGCCCATATGCCATCTAGG 59.789 57.143 0.00 0.00 41.84 3.02
3540 3928 4.474226 CCATCTAGGCGCAAGTAATTTC 57.526 45.455 10.83 0.00 41.68 2.17
3541 3929 3.251004 CCATCTAGGCGCAAGTAATTTCC 59.749 47.826 10.83 0.00 41.68 3.13
3542 3930 2.914059 TCTAGGCGCAAGTAATTTCCC 58.086 47.619 10.83 0.00 41.68 3.97
3543 3931 2.504175 TCTAGGCGCAAGTAATTTCCCT 59.496 45.455 10.83 0.00 41.68 4.20
3544 3932 1.751437 AGGCGCAAGTAATTTCCCTC 58.249 50.000 10.83 0.00 41.68 4.30
3545 3933 1.282157 AGGCGCAAGTAATTTCCCTCT 59.718 47.619 10.83 0.00 41.68 3.69
3546 3934 1.671328 GGCGCAAGTAATTTCCCTCTC 59.329 52.381 10.83 0.00 41.68 3.20
3547 3935 1.671328 GCGCAAGTAATTTCCCTCTCC 59.329 52.381 0.30 0.00 41.68 3.71
3548 3936 2.939640 GCGCAAGTAATTTCCCTCTCCA 60.940 50.000 0.30 0.00 41.68 3.86
3549 3937 2.939103 CGCAAGTAATTTCCCTCTCCAG 59.061 50.000 0.00 0.00 0.00 3.86
3550 3938 2.685388 GCAAGTAATTTCCCTCTCCAGC 59.315 50.000 0.00 0.00 0.00 4.85
3551 3939 3.873801 GCAAGTAATTTCCCTCTCCAGCA 60.874 47.826 0.00 0.00 0.00 4.41
3552 3940 4.530875 CAAGTAATTTCCCTCTCCAGCAT 58.469 43.478 0.00 0.00 0.00 3.79
3553 3941 4.162040 AGTAATTTCCCTCTCCAGCATG 57.838 45.455 0.00 0.00 0.00 4.06
3554 3942 3.782523 AGTAATTTCCCTCTCCAGCATGA 59.217 43.478 0.00 0.00 39.69 3.07
3555 3943 3.744940 AATTTCCCTCTCCAGCATGAA 57.255 42.857 0.00 0.00 39.69 2.57
3556 3944 2.795231 TTTCCCTCTCCAGCATGAAG 57.205 50.000 0.00 0.00 39.69 3.02
3557 3945 1.661463 TTCCCTCTCCAGCATGAAGT 58.339 50.000 0.00 0.00 39.69 3.01
3558 3946 1.661463 TCCCTCTCCAGCATGAAGTT 58.339 50.000 0.00 0.00 39.69 2.66
3559 3947 1.988107 TCCCTCTCCAGCATGAAGTTT 59.012 47.619 0.00 0.00 39.69 2.66
3560 3948 3.181329 TCCCTCTCCAGCATGAAGTTTA 58.819 45.455 0.00 0.00 39.69 2.01
3561 3949 3.587061 TCCCTCTCCAGCATGAAGTTTAA 59.413 43.478 0.00 0.00 39.69 1.52
3562 3950 3.691609 CCCTCTCCAGCATGAAGTTTAAC 59.308 47.826 0.00 0.00 39.69 2.01
3563 3951 4.326826 CCTCTCCAGCATGAAGTTTAACA 58.673 43.478 0.00 0.00 39.69 2.41
3564 3952 4.946157 CCTCTCCAGCATGAAGTTTAACAT 59.054 41.667 0.00 0.00 39.69 2.71
3565 3953 5.163683 CCTCTCCAGCATGAAGTTTAACATG 60.164 44.000 0.00 0.00 44.32 3.21
3566 3954 5.316167 TCTCCAGCATGAAGTTTAACATGT 58.684 37.500 0.00 0.00 43.67 3.21
3567 3955 5.412594 TCTCCAGCATGAAGTTTAACATGTC 59.587 40.000 0.00 0.00 43.67 3.06
3568 3956 4.458989 TCCAGCATGAAGTTTAACATGTCC 59.541 41.667 0.00 0.00 43.67 4.02
3569 3957 4.380867 CCAGCATGAAGTTTAACATGTCCC 60.381 45.833 0.00 0.00 43.67 4.46
3570 3958 4.460382 CAGCATGAAGTTTAACATGTCCCT 59.540 41.667 0.00 0.00 43.67 4.20
3571 3959 4.460382 AGCATGAAGTTTAACATGTCCCTG 59.540 41.667 0.00 0.00 43.67 4.45
3572 3960 4.737054 CATGAAGTTTAACATGTCCCTGC 58.263 43.478 0.00 0.00 38.98 4.85
3573 3961 4.098914 TGAAGTTTAACATGTCCCTGCT 57.901 40.909 0.00 0.00 0.00 4.24
3574 3962 4.072131 TGAAGTTTAACATGTCCCTGCTC 58.928 43.478 0.00 0.00 0.00 4.26
3575 3963 3.788227 AGTTTAACATGTCCCTGCTCA 57.212 42.857 0.00 0.00 0.00 4.26
3576 3964 4.307032 AGTTTAACATGTCCCTGCTCAT 57.693 40.909 0.00 0.00 0.00 2.90
3577 3965 5.435686 AGTTTAACATGTCCCTGCTCATA 57.564 39.130 0.00 0.00 0.00 2.15
3578 3966 6.006275 AGTTTAACATGTCCCTGCTCATAT 57.994 37.500 0.00 0.00 0.00 1.78
3579 3967 6.058183 AGTTTAACATGTCCCTGCTCATATC 58.942 40.000 0.00 0.00 0.00 1.63
3580 3968 3.498774 AACATGTCCCTGCTCATATCC 57.501 47.619 0.00 0.00 0.00 2.59
3581 3969 1.701847 ACATGTCCCTGCTCATATCCC 59.298 52.381 0.00 0.00 0.00 3.85
3582 3970 1.701292 CATGTCCCTGCTCATATCCCA 59.299 52.381 0.00 0.00 0.00 4.37
3583 3971 1.131638 TGTCCCTGCTCATATCCCAC 58.868 55.000 0.00 0.00 0.00 4.61
3584 3972 0.034059 GTCCCTGCTCATATCCCACG 59.966 60.000 0.00 0.00 0.00 4.94
3585 3973 1.121407 TCCCTGCTCATATCCCACGG 61.121 60.000 0.00 0.00 0.00 4.94
3586 3974 1.372683 CCTGCTCATATCCCACGGG 59.627 63.158 0.00 0.00 0.00 5.28
3587 3975 1.302033 CTGCTCATATCCCACGGGC 60.302 63.158 0.00 0.00 34.68 6.13
3588 3976 2.043604 CTGCTCATATCCCACGGGCA 62.044 60.000 0.00 0.00 34.68 5.36
3589 3977 1.148273 GCTCATATCCCACGGGCAA 59.852 57.895 0.00 0.00 34.68 4.52
3590 3978 0.886490 GCTCATATCCCACGGGCAAG 60.886 60.000 0.00 0.00 34.68 4.01
3591 3979 0.469917 CTCATATCCCACGGGCAAGT 59.530 55.000 0.00 0.00 34.68 3.16
3592 3980 0.180171 TCATATCCCACGGGCAAGTG 59.820 55.000 0.00 5.51 41.53 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.109359 CAGAGGTAAGTATTTCCCTCAGTTG 58.891 44.000 11.43 0.00 43.51 3.16
55 56 5.310594 CCCCAAAGAGGATAGGATGATACAA 59.689 44.000 0.00 0.00 41.22 2.41
67 68 4.610333 GTTGGTATTTCCCCAAAGAGGAT 58.390 43.478 0.00 0.00 43.30 3.24
75 76 0.036448 TTCGCGTTGGTATTTCCCCA 59.964 50.000 5.77 0.00 34.77 4.96
98 99 3.625099 GGGGACGGCTGCTACTTA 58.375 61.111 0.00 0.00 0.00 2.24
242 243 2.832129 GGAATGTAGGGTCTCTGACACA 59.168 50.000 2.71 0.00 38.63 3.72
279 280 1.605165 CTAGCCGAGCCTAGGAGGG 60.605 68.421 14.75 10.89 35.37 4.30
421 423 4.227538 CGTCGTGTCTTGATATGGATACC 58.772 47.826 0.00 0.00 0.00 2.73
463 467 1.079073 AAATGGGCAAGGGTCAGGG 59.921 57.895 0.00 0.00 0.00 4.45
542 546 7.010160 ACTCTTATGGAGATGAAACCCAAAAA 58.990 34.615 4.83 0.00 44.45 1.94
601 605 2.172930 GGGGTAAAGGATGAGGGTTCTC 59.827 54.545 0.00 0.00 40.36 2.87
603 607 1.134189 CGGGGTAAAGGATGAGGGTTC 60.134 57.143 0.00 0.00 0.00 3.62
611 615 1.137697 CCTAAGCCGGGGTAAAGGAT 58.862 55.000 18.20 0.00 0.00 3.24
628 632 0.824759 GTCTCAACATAGCCGGTCCT 59.175 55.000 1.90 0.00 0.00 3.85
833 998 3.304458 CCCAGTTCTTTTAACTTGTCGGC 60.304 47.826 0.00 0.00 0.00 5.54
836 1001 5.515797 AAGCCCAGTTCTTTTAACTTGTC 57.484 39.130 0.00 0.00 0.00 3.18
1436 1609 1.333636 ATGAGGAGAAGGCCGGACTG 61.334 60.000 12.91 0.00 0.00 3.51
1464 1637 1.853319 CACACGAAGCAACGAGGTC 59.147 57.895 9.33 0.00 37.03 3.85
1488 1661 1.580942 CTCCGACCCGTCACGTTAA 59.419 57.895 0.00 0.00 0.00 2.01
1773 1950 4.325472 GCAAGCAATGTTCTTAGTGCAATC 59.675 41.667 0.00 0.00 43.53 2.67
1832 2009 2.560105 ACCTAGTCCACAAGTACCGAAC 59.440 50.000 0.00 0.00 0.00 3.95
2022 2201 9.947669 CTGAATCATGAATCTAAGATCCAAAAC 57.052 33.333 11.94 0.00 0.00 2.43
2097 2277 5.003804 GGAAAGTCCAGTGCTTGAGAATAA 58.996 41.667 0.00 0.00 36.28 1.40
2118 2299 4.478317 ACAAATTATGACTCATCTGGGGGA 59.522 41.667 0.00 0.00 0.00 4.81
2294 2475 2.882137 CCTAGTCTTCTTCTCCCTAGCG 59.118 54.545 0.00 0.00 0.00 4.26
2351 2532 5.628797 TGATGCATGAATGTACCTCCTTA 57.371 39.130 2.46 0.00 0.00 2.69
2495 2676 2.299993 TAGCCTTGATCAACTCAGCG 57.700 50.000 3.38 0.00 34.68 5.18
2498 2679 4.625028 CATCGATAGCCTTGATCAACTCA 58.375 43.478 3.38 0.00 0.00 3.41
2747 2928 3.089284 CAACAAAGGGGATGGTACTTCC 58.911 50.000 6.80 6.80 0.00 3.46
2777 2958 4.329801 CGACGATGGATCAAGAAAATGTCA 59.670 41.667 0.00 0.00 0.00 3.58
2794 3055 3.243737 TGCAGCCTGAATAATACGACGAT 60.244 43.478 0.00 0.00 0.00 3.73
2870 3210 4.261994 GCAAATTCATACCACAACACCTGT 60.262 41.667 0.00 0.00 39.56 4.00
2887 3227 8.677300 CATATACTGTTGACCTACTTGCAAATT 58.323 33.333 0.00 0.00 0.00 1.82
2912 3253 3.054139 AGCTCTGCAAATAAGGATCACCA 60.054 43.478 0.00 0.00 38.94 4.17
2917 3258 3.950395 GTCCAAGCTCTGCAAATAAGGAT 59.050 43.478 0.00 0.00 0.00 3.24
2944 3285 0.887933 ATGCCCCAACGAAATCACAC 59.112 50.000 0.00 0.00 0.00 3.82
3076 3425 4.213270 TGCCAGAATAAGTGTCGTTCAAAG 59.787 41.667 0.00 0.00 0.00 2.77
3077 3426 4.130857 TGCCAGAATAAGTGTCGTTCAAA 58.869 39.130 0.00 0.00 0.00 2.69
3079 3428 3.006430 TCTGCCAGAATAAGTGTCGTTCA 59.994 43.478 0.00 0.00 0.00 3.18
3080 3429 3.585862 TCTGCCAGAATAAGTGTCGTTC 58.414 45.455 0.00 0.00 0.00 3.95
3081 3430 3.006967 ACTCTGCCAGAATAAGTGTCGTT 59.993 43.478 0.00 0.00 0.00 3.85
3083 3432 2.926200 CACTCTGCCAGAATAAGTGTCG 59.074 50.000 0.00 0.00 34.14 4.35
3084 3433 2.675348 GCACTCTGCCAGAATAAGTGTC 59.325 50.000 11.90 3.34 39.56 3.67
3157 3545 6.385649 TGCGGTTTTAGTTCAAAGAAGATT 57.614 33.333 0.00 0.00 0.00 2.40
3158 3546 6.183360 TGTTGCGGTTTTAGTTCAAAGAAGAT 60.183 34.615 0.00 0.00 0.00 2.40
3159 3547 5.124138 TGTTGCGGTTTTAGTTCAAAGAAGA 59.876 36.000 0.00 0.00 0.00 2.87
3160 3548 5.229260 GTGTTGCGGTTTTAGTTCAAAGAAG 59.771 40.000 0.00 0.00 0.00 2.85
3209 3597 4.263435 GGTCCAAATACCAATCCGTTACA 58.737 43.478 0.00 0.00 39.50 2.41
3231 3619 0.242825 TGTCAAGCTTACCCTCGTCG 59.757 55.000 0.00 0.00 0.00 5.12
3262 3650 4.530161 AGCTCATCAAAGACCTGACTAGTT 59.470 41.667 0.00 0.00 0.00 2.24
3289 3677 1.677637 CTCCCGCTCTAACCCAGGAC 61.678 65.000 0.00 0.00 0.00 3.85
3290 3678 1.381327 CTCCCGCTCTAACCCAGGA 60.381 63.158 0.00 0.00 0.00 3.86
3291 3679 3.095347 GCTCCCGCTCTAACCCAGG 62.095 68.421 0.00 0.00 0.00 4.45
3292 3680 2.359169 TGCTCCCGCTCTAACCCAG 61.359 63.158 0.00 0.00 36.97 4.45
3293 3681 2.284331 TGCTCCCGCTCTAACCCA 60.284 61.111 0.00 0.00 36.97 4.51
3294 3682 2.180159 TTGTGCTCCCGCTCTAACCC 62.180 60.000 0.00 0.00 36.97 4.11
3295 3683 0.741221 CTTGTGCTCCCGCTCTAACC 60.741 60.000 0.00 0.00 36.97 2.85
3296 3684 0.741221 CCTTGTGCTCCCGCTCTAAC 60.741 60.000 0.00 0.00 36.97 2.34
3297 3685 0.902984 TCCTTGTGCTCCCGCTCTAA 60.903 55.000 0.00 0.00 36.97 2.10
3298 3686 1.304962 TCCTTGTGCTCCCGCTCTA 60.305 57.895 0.00 0.00 36.97 2.43
3299 3687 2.604686 TCCTTGTGCTCCCGCTCT 60.605 61.111 0.00 0.00 36.97 4.09
3300 3688 2.125350 CTCCTTGTGCTCCCGCTC 60.125 66.667 0.00 0.00 36.97 5.03
3301 3689 1.192146 TAACTCCTTGTGCTCCCGCT 61.192 55.000 0.00 0.00 36.97 5.52
3302 3690 0.741221 CTAACTCCTTGTGCTCCCGC 60.741 60.000 0.00 0.00 0.00 6.13
3303 3691 0.741221 GCTAACTCCTTGTGCTCCCG 60.741 60.000 0.00 0.00 0.00 5.14
3304 3692 0.324943 TGCTAACTCCTTGTGCTCCC 59.675 55.000 0.00 0.00 0.00 4.30
3305 3693 2.093235 AGATGCTAACTCCTTGTGCTCC 60.093 50.000 0.00 0.00 0.00 4.70
3306 3694 3.258971 AGATGCTAACTCCTTGTGCTC 57.741 47.619 0.00 0.00 0.00 4.26
3307 3695 3.710209 AAGATGCTAACTCCTTGTGCT 57.290 42.857 0.00 0.00 0.00 4.40
3308 3696 4.022849 ACAAAAGATGCTAACTCCTTGTGC 60.023 41.667 0.00 0.00 29.29 4.57
3309 3697 5.239306 TCACAAAAGATGCTAACTCCTTGTG 59.761 40.000 16.80 16.80 39.58 3.33
3310 3698 5.376625 TCACAAAAGATGCTAACTCCTTGT 58.623 37.500 0.00 0.00 0.00 3.16
3311 3699 5.471456 ACTCACAAAAGATGCTAACTCCTTG 59.529 40.000 0.00 0.00 0.00 3.61
3312 3700 5.625150 ACTCACAAAAGATGCTAACTCCTT 58.375 37.500 0.00 0.00 0.00 3.36
3313 3701 5.234466 ACTCACAAAAGATGCTAACTCCT 57.766 39.130 0.00 0.00 0.00 3.69
3314 3702 6.091441 CACTACTCACAAAAGATGCTAACTCC 59.909 42.308 0.00 0.00 0.00 3.85
3315 3703 6.091441 CCACTACTCACAAAAGATGCTAACTC 59.909 42.308 0.00 0.00 0.00 3.01
3316 3704 5.934625 CCACTACTCACAAAAGATGCTAACT 59.065 40.000 0.00 0.00 0.00 2.24
3317 3705 5.701290 ACCACTACTCACAAAAGATGCTAAC 59.299 40.000 0.00 0.00 0.00 2.34
3318 3706 5.865085 ACCACTACTCACAAAAGATGCTAA 58.135 37.500 0.00 0.00 0.00 3.09
3319 3707 5.479306 GACCACTACTCACAAAAGATGCTA 58.521 41.667 0.00 0.00 0.00 3.49
3320 3708 4.319177 GACCACTACTCACAAAAGATGCT 58.681 43.478 0.00 0.00 0.00 3.79
3321 3709 3.123621 CGACCACTACTCACAAAAGATGC 59.876 47.826 0.00 0.00 0.00 3.91
3322 3710 4.150627 CACGACCACTACTCACAAAAGATG 59.849 45.833 0.00 0.00 0.00 2.90
3323 3711 4.202223 ACACGACCACTACTCACAAAAGAT 60.202 41.667 0.00 0.00 0.00 2.40
3324 3712 3.131577 ACACGACCACTACTCACAAAAGA 59.868 43.478 0.00 0.00 0.00 2.52
3325 3713 3.454375 ACACGACCACTACTCACAAAAG 58.546 45.455 0.00 0.00 0.00 2.27
3326 3714 3.530265 ACACGACCACTACTCACAAAA 57.470 42.857 0.00 0.00 0.00 2.44
3327 3715 3.633525 ACTACACGACCACTACTCACAAA 59.366 43.478 0.00 0.00 0.00 2.83
3328 3716 3.216800 ACTACACGACCACTACTCACAA 58.783 45.455 0.00 0.00 0.00 3.33
3329 3717 2.854963 ACTACACGACCACTACTCACA 58.145 47.619 0.00 0.00 0.00 3.58
3330 3718 3.373439 CCTACTACACGACCACTACTCAC 59.627 52.174 0.00 0.00 0.00 3.51
3331 3719 3.261643 TCCTACTACACGACCACTACTCA 59.738 47.826 0.00 0.00 0.00 3.41
3332 3720 3.866651 TCCTACTACACGACCACTACTC 58.133 50.000 0.00 0.00 0.00 2.59
3333 3721 3.262915 ACTCCTACTACACGACCACTACT 59.737 47.826 0.00 0.00 0.00 2.57
3334 3722 3.373439 CACTCCTACTACACGACCACTAC 59.627 52.174 0.00 0.00 0.00 2.73
3335 3723 3.603532 CACTCCTACTACACGACCACTA 58.396 50.000 0.00 0.00 0.00 2.74
3336 3724 2.434428 CACTCCTACTACACGACCACT 58.566 52.381 0.00 0.00 0.00 4.00
3337 3725 1.471684 CCACTCCTACTACACGACCAC 59.528 57.143 0.00 0.00 0.00 4.16
3338 3726 1.352017 TCCACTCCTACTACACGACCA 59.648 52.381 0.00 0.00 0.00 4.02
3339 3727 2.015587 CTCCACTCCTACTACACGACC 58.984 57.143 0.00 0.00 0.00 4.79
3340 3728 2.015587 CCTCCACTCCTACTACACGAC 58.984 57.143 0.00 0.00 0.00 4.34
3341 3729 1.632409 ACCTCCACTCCTACTACACGA 59.368 52.381 0.00 0.00 0.00 4.35
3342 3730 2.125773 ACCTCCACTCCTACTACACG 57.874 55.000 0.00 0.00 0.00 4.49
3343 3731 2.950975 GCTACCTCCACTCCTACTACAC 59.049 54.545 0.00 0.00 0.00 2.90
3344 3732 2.851194 AGCTACCTCCACTCCTACTACA 59.149 50.000 0.00 0.00 0.00 2.74
3345 3733 3.215975 CAGCTACCTCCACTCCTACTAC 58.784 54.545 0.00 0.00 0.00 2.73
3346 3734 2.175069 CCAGCTACCTCCACTCCTACTA 59.825 54.545 0.00 0.00 0.00 1.82
3347 3735 1.063567 CCAGCTACCTCCACTCCTACT 60.064 57.143 0.00 0.00 0.00 2.57
3348 3736 1.404843 CCAGCTACCTCCACTCCTAC 58.595 60.000 0.00 0.00 0.00 3.18
3349 3737 0.261991 CCCAGCTACCTCCACTCCTA 59.738 60.000 0.00 0.00 0.00 2.94
3350 3738 1.002274 CCCAGCTACCTCCACTCCT 59.998 63.158 0.00 0.00 0.00 3.69
3351 3739 2.736826 GCCCAGCTACCTCCACTCC 61.737 68.421 0.00 0.00 0.00 3.85
3352 3740 2.736826 GGCCCAGCTACCTCCACTC 61.737 68.421 0.00 0.00 0.00 3.51
3353 3741 2.689034 GGCCCAGCTACCTCCACT 60.689 66.667 0.00 0.00 0.00 4.00
3354 3742 4.162690 CGGCCCAGCTACCTCCAC 62.163 72.222 0.00 0.00 0.00 4.02
3369 3757 3.663176 CACACAAGCACCAGCCGG 61.663 66.667 0.00 0.00 43.56 6.13
3370 3758 2.901840 ACACACAAGCACCAGCCG 60.902 61.111 0.00 0.00 43.56 5.52
3371 3759 2.723746 CACACACAAGCACCAGCC 59.276 61.111 0.00 0.00 43.56 4.85
3372 3760 2.026590 GCACACACAAGCACCAGC 59.973 61.111 0.00 0.00 42.56 4.85
3373 3761 1.357690 CAGCACACACAAGCACCAG 59.642 57.895 0.00 0.00 0.00 4.00
3374 3762 2.773745 GCAGCACACACAAGCACCA 61.774 57.895 0.00 0.00 0.00 4.17
3375 3763 1.165907 TAGCAGCACACACAAGCACC 61.166 55.000 0.00 0.00 0.00 5.01
3376 3764 0.236711 CTAGCAGCACACACAAGCAC 59.763 55.000 0.00 0.00 0.00 4.40
3377 3765 0.106521 TCTAGCAGCACACACAAGCA 59.893 50.000 0.00 0.00 0.00 3.91
3378 3766 0.795085 CTCTAGCAGCACACACAAGC 59.205 55.000 0.00 0.00 0.00 4.01
3387 3775 7.143555 TGATTACATCAAGGCTCTAGCAGCA 62.144 44.000 13.76 0.00 42.70 4.41
3388 3776 4.741837 TGATTACATCAAGGCTCTAGCAGC 60.742 45.833 4.07 5.83 41.21 5.25
3389 3777 4.953667 TGATTACATCAAGGCTCTAGCAG 58.046 43.478 4.07 0.00 38.51 4.24
3390 3778 5.557576 ATGATTACATCAAGGCTCTAGCA 57.442 39.130 4.07 0.00 43.50 3.49
3391 3779 6.696411 AGTATGATTACATCAAGGCTCTAGC 58.304 40.000 0.00 0.00 43.50 3.42
3392 3780 8.121305 AGAGTATGATTACATCAAGGCTCTAG 57.879 38.462 12.46 0.00 43.50 2.43
3393 3781 8.363390 CAAGAGTATGATTACATCAAGGCTCTA 58.637 37.037 13.60 0.00 43.50 2.43
3394 3782 6.992664 AGAGTATGATTACATCAAGGCTCT 57.007 37.500 10.04 10.04 43.50 4.09
3395 3783 6.989169 ACAAGAGTATGATTACATCAAGGCTC 59.011 38.462 0.00 0.38 43.50 4.70
3396 3784 6.893583 ACAAGAGTATGATTACATCAAGGCT 58.106 36.000 0.00 0.00 43.50 4.58
3397 3785 7.710907 TGTACAAGAGTATGATTACATCAAGGC 59.289 37.037 0.00 0.00 43.50 4.35
3398 3786 9.770097 ATGTACAAGAGTATGATTACATCAAGG 57.230 33.333 0.00 0.00 43.50 3.61
3407 3795 9.277783 GGCAGAAATATGTACAAGAGTATGATT 57.722 33.333 0.00 0.00 31.84 2.57
3408 3796 8.654997 AGGCAGAAATATGTACAAGAGTATGAT 58.345 33.333 0.00 0.00 31.84 2.45
3409 3797 8.023021 AGGCAGAAATATGTACAAGAGTATGA 57.977 34.615 0.00 0.00 31.84 2.15
3410 3798 7.386299 GGAGGCAGAAATATGTACAAGAGTATG 59.614 40.741 0.00 0.00 31.84 2.39
3411 3799 7.291182 AGGAGGCAGAAATATGTACAAGAGTAT 59.709 37.037 0.00 0.00 31.84 2.12
3412 3800 6.611642 AGGAGGCAGAAATATGTACAAGAGTA 59.388 38.462 0.00 0.00 0.00 2.59
3413 3801 5.426833 AGGAGGCAGAAATATGTACAAGAGT 59.573 40.000 0.00 0.00 0.00 3.24
3414 3802 5.923204 AGGAGGCAGAAATATGTACAAGAG 58.077 41.667 0.00 0.00 0.00 2.85
3415 3803 5.957771 AGGAGGCAGAAATATGTACAAGA 57.042 39.130 0.00 0.00 0.00 3.02
3416 3804 9.778741 TTTATAGGAGGCAGAAATATGTACAAG 57.221 33.333 0.00 0.00 0.00 3.16
3417 3805 9.778741 CTTTATAGGAGGCAGAAATATGTACAA 57.221 33.333 0.00 0.00 0.00 2.41
3418 3806 7.878127 GCTTTATAGGAGGCAGAAATATGTACA 59.122 37.037 0.00 0.00 0.00 2.90
3419 3807 7.334671 GGCTTTATAGGAGGCAGAAATATGTAC 59.665 40.741 6.82 0.00 39.31 2.90
3420 3808 7.017155 TGGCTTTATAGGAGGCAGAAATATGTA 59.983 37.037 9.47 0.00 43.69 2.29
3421 3809 6.183361 TGGCTTTATAGGAGGCAGAAATATGT 60.183 38.462 9.47 0.00 43.69 2.29
3422 3810 6.240894 TGGCTTTATAGGAGGCAGAAATATG 58.759 40.000 9.47 0.00 43.69 1.78
3423 3811 6.454223 TGGCTTTATAGGAGGCAGAAATAT 57.546 37.500 9.47 0.00 43.69 1.28
3424 3812 5.904984 TGGCTTTATAGGAGGCAGAAATA 57.095 39.130 9.47 0.00 43.69 1.40
3425 3813 4.796110 TGGCTTTATAGGAGGCAGAAAT 57.204 40.909 9.47 0.00 43.69 2.17
3430 3818 2.487775 TCCTTGGCTTTATAGGAGGCA 58.512 47.619 9.47 9.47 46.39 4.75
3431 3819 3.215151 GTTCCTTGGCTTTATAGGAGGC 58.785 50.000 0.00 5.21 39.15 4.70
3432 3820 3.467803 CGTTCCTTGGCTTTATAGGAGG 58.532 50.000 0.00 0.00 39.15 4.30
3433 3821 2.872858 GCGTTCCTTGGCTTTATAGGAG 59.127 50.000 0.00 0.00 39.15 3.69
3434 3822 2.740580 CGCGTTCCTTGGCTTTATAGGA 60.741 50.000 0.00 0.00 36.31 2.94
3435 3823 1.597663 CGCGTTCCTTGGCTTTATAGG 59.402 52.381 0.00 0.00 0.00 2.57
3436 3824 2.546778 TCGCGTTCCTTGGCTTTATAG 58.453 47.619 5.77 0.00 0.00 1.31
3437 3825 2.676632 TCGCGTTCCTTGGCTTTATA 57.323 45.000 5.77 0.00 0.00 0.98
3438 3826 2.038387 ATCGCGTTCCTTGGCTTTAT 57.962 45.000 5.77 0.00 0.00 1.40
3439 3827 1.466950 CAATCGCGTTCCTTGGCTTTA 59.533 47.619 5.77 0.00 0.00 1.85
3440 3828 0.240945 CAATCGCGTTCCTTGGCTTT 59.759 50.000 5.77 0.00 0.00 3.51
3441 3829 1.875963 CAATCGCGTTCCTTGGCTT 59.124 52.632 5.77 0.00 0.00 4.35
3442 3830 2.690778 GCAATCGCGTTCCTTGGCT 61.691 57.895 5.77 0.00 0.00 4.75
3443 3831 2.202479 GCAATCGCGTTCCTTGGC 60.202 61.111 5.77 0.00 0.00 4.52
3453 3841 3.658351 AAATTGAGAGTACGCAATCGC 57.342 42.857 10.59 0.00 43.50 4.58
3500 3888 3.987745 TGGCATATGGGCTCCTTAAAAA 58.012 40.909 4.56 0.00 43.83 1.94
3501 3889 3.678965 TGGCATATGGGCTCCTTAAAA 57.321 42.857 4.56 0.00 43.83 1.52
3502 3890 3.398967 AGATGGCATATGGGCTCCTTAAA 59.601 43.478 0.00 0.00 43.83 1.52
3503 3891 2.988859 AGATGGCATATGGGCTCCTTAA 59.011 45.455 0.00 0.00 43.83 1.85
3504 3892 2.636005 AGATGGCATATGGGCTCCTTA 58.364 47.619 0.00 0.00 43.83 2.69
3505 3893 1.453633 AGATGGCATATGGGCTCCTT 58.546 50.000 0.00 0.00 43.83 3.36
3506 3894 2.194859 CTAGATGGCATATGGGCTCCT 58.805 52.381 4.57 0.00 43.83 3.69
3507 3895 1.211457 CCTAGATGGCATATGGGCTCC 59.789 57.143 11.71 0.00 43.83 4.70
3508 3896 2.706339 CCTAGATGGCATATGGGCTC 57.294 55.000 11.71 0.00 43.83 4.70
3519 3907 3.251004 GGAAATTACTTGCGCCTAGATGG 59.749 47.826 4.18 0.00 39.35 3.51
3520 3908 3.251004 GGGAAATTACTTGCGCCTAGATG 59.749 47.826 4.18 0.00 0.00 2.90
3521 3909 3.136626 AGGGAAATTACTTGCGCCTAGAT 59.863 43.478 4.18 0.00 0.00 1.98
3522 3910 2.504175 AGGGAAATTACTTGCGCCTAGA 59.496 45.455 4.18 0.00 0.00 2.43
3523 3911 2.872858 GAGGGAAATTACTTGCGCCTAG 59.127 50.000 4.18 4.80 0.00 3.02
3524 3912 2.504175 AGAGGGAAATTACTTGCGCCTA 59.496 45.455 4.18 0.00 0.00 3.93
3525 3913 1.282157 AGAGGGAAATTACTTGCGCCT 59.718 47.619 4.18 0.00 0.00 5.52
3526 3914 1.671328 GAGAGGGAAATTACTTGCGCC 59.329 52.381 4.18 0.00 0.00 6.53
3527 3915 1.671328 GGAGAGGGAAATTACTTGCGC 59.329 52.381 0.00 0.00 0.00 6.09
3528 3916 2.939103 CTGGAGAGGGAAATTACTTGCG 59.061 50.000 0.00 0.00 0.00 4.85
3529 3917 2.685388 GCTGGAGAGGGAAATTACTTGC 59.315 50.000 0.00 0.00 0.00 4.01
3530 3918 3.955471 TGCTGGAGAGGGAAATTACTTG 58.045 45.455 0.00 0.00 0.00 3.16
3531 3919 4.228210 TCATGCTGGAGAGGGAAATTACTT 59.772 41.667 0.00 0.00 0.00 2.24
3532 3920 3.782523 TCATGCTGGAGAGGGAAATTACT 59.217 43.478 0.00 0.00 0.00 2.24
3533 3921 4.156455 TCATGCTGGAGAGGGAAATTAC 57.844 45.455 0.00 0.00 0.00 1.89
3534 3922 4.228210 ACTTCATGCTGGAGAGGGAAATTA 59.772 41.667 0.00 0.00 0.00 1.40
3535 3923 3.011032 ACTTCATGCTGGAGAGGGAAATT 59.989 43.478 0.00 0.00 0.00 1.82
3536 3924 2.579860 ACTTCATGCTGGAGAGGGAAAT 59.420 45.455 0.00 0.00 0.00 2.17
3537 3925 1.988107 ACTTCATGCTGGAGAGGGAAA 59.012 47.619 0.00 0.00 0.00 3.13
3538 3926 1.661463 ACTTCATGCTGGAGAGGGAA 58.339 50.000 0.00 0.00 0.00 3.97
3539 3927 1.661463 AACTTCATGCTGGAGAGGGA 58.339 50.000 0.00 0.00 0.00 4.20
3540 3928 2.503895 AAACTTCATGCTGGAGAGGG 57.496 50.000 0.00 0.00 0.00 4.30
3541 3929 4.326826 TGTTAAACTTCATGCTGGAGAGG 58.673 43.478 0.00 0.00 0.00 3.69
3542 3930 5.413833 ACATGTTAAACTTCATGCTGGAGAG 59.586 40.000 0.00 0.00 43.34 3.20
3543 3931 5.316167 ACATGTTAAACTTCATGCTGGAGA 58.684 37.500 0.00 0.00 43.34 3.71
3544 3932 5.392380 GGACATGTTAAACTTCATGCTGGAG 60.392 44.000 0.00 0.00 43.34 3.86
3545 3933 4.458989 GGACATGTTAAACTTCATGCTGGA 59.541 41.667 0.00 0.00 43.34 3.86
3546 3934 4.380867 GGGACATGTTAAACTTCATGCTGG 60.381 45.833 0.00 0.00 43.34 4.85
3547 3935 4.460382 AGGGACATGTTAAACTTCATGCTG 59.540 41.667 0.00 0.00 43.34 4.41
3548 3936 4.460382 CAGGGACATGTTAAACTTCATGCT 59.540 41.667 0.00 0.00 43.34 3.79
3549 3937 4.737054 CAGGGACATGTTAAACTTCATGC 58.263 43.478 0.00 0.00 43.34 4.06
3550 3938 4.460382 AGCAGGGACATGTTAAACTTCATG 59.540 41.667 0.00 0.00 44.56 3.07
3551 3939 4.666512 AGCAGGGACATGTTAAACTTCAT 58.333 39.130 0.00 0.00 0.00 2.57
3552 3940 4.072131 GAGCAGGGACATGTTAAACTTCA 58.928 43.478 0.00 0.00 0.00 3.02
3553 3941 4.072131 TGAGCAGGGACATGTTAAACTTC 58.928 43.478 0.00 0.00 0.00 3.01
3554 3942 4.098914 TGAGCAGGGACATGTTAAACTT 57.901 40.909 0.00 0.00 0.00 2.66
3555 3943 3.788227 TGAGCAGGGACATGTTAAACT 57.212 42.857 0.00 0.00 0.00 2.66
3556 3944 5.239525 GGATATGAGCAGGGACATGTTAAAC 59.760 44.000 0.00 0.00 0.00 2.01
3557 3945 5.376625 GGATATGAGCAGGGACATGTTAAA 58.623 41.667 0.00 0.00 0.00 1.52
3558 3946 4.202461 GGGATATGAGCAGGGACATGTTAA 60.202 45.833 0.00 0.00 0.00 2.01
3559 3947 3.327757 GGGATATGAGCAGGGACATGTTA 59.672 47.826 0.00 0.00 0.00 2.41
3560 3948 2.107204 GGGATATGAGCAGGGACATGTT 59.893 50.000 0.00 0.00 0.00 2.71
3561 3949 1.701847 GGGATATGAGCAGGGACATGT 59.298 52.381 0.00 0.00 0.00 3.21
3562 3950 1.701292 TGGGATATGAGCAGGGACATG 59.299 52.381 0.00 0.00 0.00 3.21
3563 3951 1.701847 GTGGGATATGAGCAGGGACAT 59.298 52.381 0.00 0.00 0.00 3.06
3564 3952 1.131638 GTGGGATATGAGCAGGGACA 58.868 55.000 0.00 0.00 0.00 4.02
3565 3953 0.034059 CGTGGGATATGAGCAGGGAC 59.966 60.000 0.00 0.00 0.00 4.46
3566 3954 1.121407 CCGTGGGATATGAGCAGGGA 61.121 60.000 0.00 0.00 0.00 4.20
3567 3955 1.372683 CCGTGGGATATGAGCAGGG 59.627 63.158 0.00 0.00 0.00 4.45
3568 3956 1.372683 CCCGTGGGATATGAGCAGG 59.627 63.158 0.00 0.00 37.50 4.85
3569 3957 1.302033 GCCCGTGGGATATGAGCAG 60.302 63.158 9.72 0.00 37.50 4.24
3570 3958 1.631071 TTGCCCGTGGGATATGAGCA 61.631 55.000 9.72 0.00 37.50 4.26
3571 3959 0.886490 CTTGCCCGTGGGATATGAGC 60.886 60.000 9.72 0.00 37.50 4.26
3572 3960 0.469917 ACTTGCCCGTGGGATATGAG 59.530 55.000 9.72 0.86 37.50 2.90
3573 3961 0.180171 CACTTGCCCGTGGGATATGA 59.820 55.000 9.72 0.00 37.50 2.15
3574 3962 2.706636 CACTTGCCCGTGGGATATG 58.293 57.895 9.72 1.83 37.50 1.78


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

AutoCloner maintained by Alex Coulton.