Multiple sequence alignment - TraesCS3D01G355200

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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 TraesCS3D01G355200 chr3D 100.000 3881 0 0 1 3881 466681158 466677278 0.000000e+00 7167.0
1 TraesCS3D01G355200 chr3D 99.174 242 2 0 3413 3654 94886844 94886603 1.660000e-118 436.0
2 TraesCS3D01G355200 chr3D 99.170 241 2 0 3414 3654 327381717 327381957 5.950000e-118 435.0
3 TraesCS3D01G355200 chr3D 98.374 246 3 1 3410 3655 129016827 129016583 7.700000e-117 431.0
4 TraesCS3D01G355200 chr3D 98.760 242 3 0 3413 3654 603126593 603126352 7.700000e-117 431.0
5 TraesCS3D01G355200 chr3D 98.760 242 3 0 3413 3654 611242276 611242035 7.700000e-117 431.0
6 TraesCS3D01G355200 chr3D 92.188 64 3 2 457 518 381994036 381993973 5.340000e-14 89.8
7 TraesCS3D01G355200 chr3B 94.152 3300 137 30 1 3284 620456967 620453708 0.000000e+00 4974.0
8 TraesCS3D01G355200 chr3B 82.857 105 6 5 415 518 497713545 497713452 2.480000e-12 84.2
9 TraesCS3D01G355200 chr3A 95.651 2690 81 18 735 3415 609689066 609686404 0.000000e+00 4287.0
10 TraesCS3D01G355200 chr3A 87.571 885 64 18 8 886 609694895 609694051 0.000000e+00 983.0
11 TraesCS3D01G355200 chr3A 94.709 189 10 0 889 1077 609693284 609693096 1.050000e-75 294.0
12 TraesCS3D01G355200 chr3A 86.425 221 27 2 3653 3873 609686405 609686188 5.010000e-59 239.0
13 TraesCS3D01G355200 chr5D 83.191 821 111 22 1085 1884 501095795 501096609 0.000000e+00 726.0
14 TraesCS3D01G355200 chr5D 82.540 756 125 5 2047 2801 501096772 501097521 0.000000e+00 658.0
15 TraesCS3D01G355200 chr5D 98.367 245 4 0 3414 3658 112358172 112357928 7.700000e-117 431.0
16 TraesCS3D01G355200 chr7A 82.698 734 114 11 1155 1880 726605945 726605217 1.180000e-179 640.0
17 TraesCS3D01G355200 chr7A 82.698 734 114 11 1155 1880 727276733 727277461 1.180000e-179 640.0
18 TraesCS3D01G355200 chr7A 81.583 733 122 11 1155 1879 682899102 682898375 9.280000e-166 593.0
19 TraesCS3D01G355200 chr5B 82.210 742 124 3 2048 2788 622605440 622606174 1.970000e-177 632.0
20 TraesCS3D01G355200 chr6D 81.830 765 110 21 2016 2776 58855740 58855001 1.980000e-172 616.0
21 TraesCS3D01G355200 chr5A 81.806 742 125 5 2047 2786 626119942 626119209 7.130000e-172 614.0
22 TraesCS3D01G355200 chr7B 81.880 734 120 11 1155 1880 685666829 685667557 1.190000e-169 606.0
23 TraesCS3D01G355200 chr7B 81.855 733 120 11 1155 1879 671702154 671702881 4.290000e-169 604.0
24 TraesCS3D01G355200 chr4D 81.462 766 113 21 2015 2776 133469861 133470601 5.550000e-168 601.0
25 TraesCS3D01G355200 chr4D 97.600 250 5 1 3407 3655 226543472 226543721 9.960000e-116 427.0
26 TraesCS3D01G355200 chr6A 81.356 767 114 21 2014 2776 74905899 74905158 7.180000e-167 597.0
27 TraesCS3D01G355200 chr7D 81.583 733 122 11 1155 1879 591814425 591813698 9.280000e-166 593.0
28 TraesCS3D01G355200 chr4A 81.120 768 114 23 2014 2776 428163974 428163233 1.550000e-163 586.0
29 TraesCS3D01G355200 chr4A 86.022 93 12 1 464 555 593194187 593194279 8.870000e-17 99.0
30 TraesCS3D01G355200 chr6B 81.046 765 116 19 2016 2776 132431451 132430712 2.010000e-162 582.0
31 TraesCS3D01G355200 chr1D 99.592 245 1 0 3410 3654 16232237 16231993 7.650000e-122 448.0
32 TraesCS3D01G355200 chr1D 98.765 243 3 0 3413 3655 203950133 203949891 2.140000e-117 433.0
33 TraesCS3D01G355200 chr2D 78.788 231 34 10 316 534 590326127 590325900 1.450000e-29 141.0


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 TraesCS3D01G355200 chr3D 466677278 466681158 3880 True 7167.0 7167 100.0000 1 3881 1 chr3D.!!$R4 3880
1 TraesCS3D01G355200 chr3B 620453708 620456967 3259 True 4974.0 4974 94.1520 1 3284 1 chr3B.!!$R2 3283
2 TraesCS3D01G355200 chr3A 609686188 609689066 2878 True 2263.0 4287 91.0380 735 3873 2 chr3A.!!$R1 3138
3 TraesCS3D01G355200 chr3A 609693096 609694895 1799 True 638.5 983 91.1400 8 1077 2 chr3A.!!$R2 1069
4 TraesCS3D01G355200 chr5D 501095795 501097521 1726 False 692.0 726 82.8655 1085 2801 2 chr5D.!!$F1 1716
5 TraesCS3D01G355200 chr7A 726605217 726605945 728 True 640.0 640 82.6980 1155 1880 1 chr7A.!!$R2 725
6 TraesCS3D01G355200 chr7A 727276733 727277461 728 False 640.0 640 82.6980 1155 1880 1 chr7A.!!$F1 725
7 TraesCS3D01G355200 chr7A 682898375 682899102 727 True 593.0 593 81.5830 1155 1879 1 chr7A.!!$R1 724
8 TraesCS3D01G355200 chr5B 622605440 622606174 734 False 632.0 632 82.2100 2048 2788 1 chr5B.!!$F1 740
9 TraesCS3D01G355200 chr6D 58855001 58855740 739 True 616.0 616 81.8300 2016 2776 1 chr6D.!!$R1 760
10 TraesCS3D01G355200 chr5A 626119209 626119942 733 True 614.0 614 81.8060 2047 2786 1 chr5A.!!$R1 739
11 TraesCS3D01G355200 chr7B 685666829 685667557 728 False 606.0 606 81.8800 1155 1880 1 chr7B.!!$F2 725
12 TraesCS3D01G355200 chr7B 671702154 671702881 727 False 604.0 604 81.8550 1155 1879 1 chr7B.!!$F1 724
13 TraesCS3D01G355200 chr4D 133469861 133470601 740 False 601.0 601 81.4620 2015 2776 1 chr4D.!!$F1 761
14 TraesCS3D01G355200 chr6A 74905158 74905899 741 True 597.0 597 81.3560 2014 2776 1 chr6A.!!$R1 762
15 TraesCS3D01G355200 chr7D 591813698 591814425 727 True 593.0 593 81.5830 1155 1879 1 chr7D.!!$R1 724
16 TraesCS3D01G355200 chr4A 428163233 428163974 741 True 586.0 586 81.1200 2014 2776 1 chr4A.!!$R1 762
17 TraesCS3D01G355200 chr6B 132430712 132431451 739 True 582.0 582 81.0460 2016 2776 1 chr6B.!!$R1 760

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
696 703 0.673644 CGTCTGCCGTGATTTCCCTT 60.674 55.0 0.0 0.0 0.0 3.95 F
1611 2402 0.179089 CCAAGTCGCTCATCCTCCTG 60.179 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 3401 2.749044 TCGGCGTCGTAGAGCCTT 60.749 61.111 10.18 0.0 44.62 4.35 R
3451 4288 0.041312 CGGTCAAAGTTGAAGCACGG 60.041 55.000 0.00 0.0 39.21 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.974010 GGTCTCCCGGTCCACACATA 60.974 60.000 0.00 0.00 0.00 2.29
254 255 2.173669 CGCTCGATCCACCGCAAAT 61.174 57.895 0.00 0.00 0.00 2.32
257 258 1.668751 GCTCGATCCACCGCAAATAAA 59.331 47.619 0.00 0.00 0.00 1.40
336 342 7.258022 ACCATGGTTTAAATTTCAGTTTTGC 57.742 32.000 13.00 0.00 0.00 3.68
532 539 9.653287 TTGACAGAAAGACGAATATTTCAGTAT 57.347 29.630 0.00 0.00 36.32 2.12
559 566 7.411804 GCACCGAAATTACTGAATTTTCAATGG 60.412 37.037 0.00 0.00 43.76 3.16
683 690 3.300667 CTTCTTGGCGCACGTCTGC 62.301 63.158 10.83 0.00 40.38 4.26
696 703 0.673644 CGTCTGCCGTGATTTCCCTT 60.674 55.000 0.00 0.00 0.00 3.95
699 706 2.418976 GTCTGCCGTGATTTCCCTTTAC 59.581 50.000 0.00 0.00 0.00 2.01
702 709 1.375551 CCGTGATTTCCCTTTACCGG 58.624 55.000 0.00 0.00 0.00 5.28
729 737 2.033675 TGAGTGCACATTTGTCAAGCTG 59.966 45.455 21.04 0.00 0.00 4.24
780 788 1.314730 ACGTGTGTGAAACCCCAATC 58.685 50.000 0.00 0.00 34.36 2.67
826 835 7.483307 TGTGAAAGAATCCTTTTCACTCAAAG 58.517 34.615 23.29 0.00 42.30 2.77
903 1682 7.535489 ACAAACTTATTACGACCAAGATAGC 57.465 36.000 0.00 0.00 0.00 2.97
905 1684 7.277981 ACAAACTTATTACGACCAAGATAGCAG 59.722 37.037 0.00 0.00 0.00 4.24
1193 1984 2.101582 ACATCTTCGGCATCTACTCCAC 59.898 50.000 0.00 0.00 0.00 4.02
1291 2082 4.516195 GCGTCTTCTCGGGGCTCC 62.516 72.222 0.00 0.00 0.00 4.70
1332 2123 2.742372 GTCGTGCTCGCCATTGGT 60.742 61.111 4.26 0.00 36.96 3.67
1611 2402 0.179089 CCAAGTCGCTCATCCTCCTG 60.179 60.000 0.00 0.00 0.00 3.86
2391 3221 4.933064 GTCCTGATCGCGCTCGGG 62.933 72.222 27.96 27.96 42.23 5.14
2938 3768 1.195448 CTGAAGCAGCAACCTAACACG 59.805 52.381 0.00 0.00 0.00 4.49
3100 3937 1.888512 CATGGCGCATATTAAAGGGCT 59.111 47.619 10.83 0.00 42.56 5.19
3116 3953 1.064458 GCTAGAGAAGGACGCCGTC 59.936 63.158 9.15 9.15 32.29 4.79
3162 3999 1.751927 GGTCCTGCTTGATGCCAGG 60.752 63.158 0.31 0.31 42.00 4.45
3211 4048 1.713937 CGTTGCACTGCACCAAGTCA 61.714 55.000 2.26 0.00 38.71 3.41
3269 4106 6.289064 ACCGTATGAGTCAAGTCTTTCTTTT 58.711 36.000 0.00 0.00 33.63 2.27
3293 4130 3.560882 CCCTCTTGCAAGGAGATTGAAGT 60.561 47.826 25.73 0.00 41.83 3.01
3298 4135 7.206981 TCTTGCAAGGAGATTGAAGTAAAAG 57.793 36.000 25.73 0.00 41.83 2.27
3303 4140 6.870439 GCAAGGAGATTGAAGTAAAAGCATTT 59.130 34.615 0.00 0.00 41.83 2.32
3318 4155 5.911378 AAGCATTTCTTCCCTTGATCTTC 57.089 39.130 0.00 0.00 0.00 2.87
3353 4190 1.661112 GAATTCGCCTCCTCTTTGTCG 59.339 52.381 0.00 0.00 0.00 4.35
3415 4252 2.149578 TCGGCTTCGGCTAGTAGATAC 58.850 52.381 0.00 0.00 41.44 2.24
3416 4253 2.152830 CGGCTTCGGCTAGTAGATACT 58.847 52.381 0.00 0.00 41.44 2.12
3417 4254 2.160022 CGGCTTCGGCTAGTAGATACTC 59.840 54.545 0.00 0.00 41.44 2.59
3418 4255 2.488937 GGCTTCGGCTAGTAGATACTCC 59.511 54.545 0.00 0.00 41.44 3.85
3419 4256 2.488937 GCTTCGGCTAGTAGATACTCCC 59.511 54.545 0.00 0.00 37.73 4.30
3420 4257 3.811454 GCTTCGGCTAGTAGATACTCCCT 60.811 52.174 0.00 0.00 37.73 4.20
3421 4258 3.699411 TCGGCTAGTAGATACTCCCTC 57.301 52.381 0.00 0.00 37.73 4.30
3422 4259 2.305343 TCGGCTAGTAGATACTCCCTCC 59.695 54.545 0.00 0.00 37.73 4.30
3423 4260 2.040012 CGGCTAGTAGATACTCCCTCCA 59.960 54.545 0.00 0.00 37.73 3.86
3424 4261 3.308545 CGGCTAGTAGATACTCCCTCCAT 60.309 52.174 0.00 0.00 37.73 3.41
3425 4262 4.679331 GGCTAGTAGATACTCCCTCCATT 58.321 47.826 0.00 0.00 37.73 3.16
3426 4263 4.707934 GGCTAGTAGATACTCCCTCCATTC 59.292 50.000 0.00 0.00 37.73 2.67
3427 4264 4.707934 GCTAGTAGATACTCCCTCCATTCC 59.292 50.000 0.00 0.00 37.73 3.01
3428 4265 4.834406 AGTAGATACTCCCTCCATTCCA 57.166 45.455 0.00 0.00 0.00 3.53
3429 4266 4.484912 AGTAGATACTCCCTCCATTCCAC 58.515 47.826 0.00 0.00 0.00 4.02
3430 4267 3.421394 AGATACTCCCTCCATTCCACA 57.579 47.619 0.00 0.00 0.00 4.17
3431 4268 3.736094 AGATACTCCCTCCATTCCACAA 58.264 45.455 0.00 0.00 0.00 3.33
3432 4269 4.310740 AGATACTCCCTCCATTCCACAAT 58.689 43.478 0.00 0.00 0.00 2.71
3433 4270 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
3434 4271 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
3435 4272 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
3436 4273 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
3437 4274 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
3438 4275 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
3439 4276 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
3440 4277 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
3441 4278 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
3442 4279 4.009675 TCCATTCCACAATGTAGTGCTTC 58.990 43.478 0.00 0.00 38.22 3.86
3443 4280 3.129287 CCATTCCACAATGTAGTGCTTCC 59.871 47.826 0.00 0.00 38.22 3.46
3444 4281 3.788227 TTCCACAATGTAGTGCTTCCT 57.212 42.857 0.00 0.00 38.18 3.36
3445 4282 3.334583 TCCACAATGTAGTGCTTCCTC 57.665 47.619 0.00 0.00 38.18 3.71
3446 4283 2.906389 TCCACAATGTAGTGCTTCCTCT 59.094 45.455 0.00 0.00 38.18 3.69
3447 4284 4.093743 TCCACAATGTAGTGCTTCCTCTA 58.906 43.478 0.00 0.00 38.18 2.43
3448 4285 4.716784 TCCACAATGTAGTGCTTCCTCTAT 59.283 41.667 0.00 0.00 38.18 1.98
3449 4286 5.053145 CCACAATGTAGTGCTTCCTCTATC 58.947 45.833 0.00 0.00 38.18 2.08
3450 4287 5.163364 CCACAATGTAGTGCTTCCTCTATCT 60.163 44.000 0.00 0.00 38.18 1.98
3451 4288 5.982516 CACAATGTAGTGCTTCCTCTATCTC 59.017 44.000 0.00 0.00 32.04 2.75
3452 4289 5.069781 ACAATGTAGTGCTTCCTCTATCTCC 59.930 44.000 0.00 0.00 0.00 3.71
3453 4290 3.215151 TGTAGTGCTTCCTCTATCTCCG 58.785 50.000 0.00 0.00 0.00 4.63
3454 4291 2.445682 AGTGCTTCCTCTATCTCCGT 57.554 50.000 0.00 0.00 0.00 4.69
3455 4292 2.028130 AGTGCTTCCTCTATCTCCGTG 58.972 52.381 0.00 0.00 0.00 4.94
3456 4293 0.747255 TGCTTCCTCTATCTCCGTGC 59.253 55.000 0.00 0.00 0.00 5.34
3457 4294 1.036707 GCTTCCTCTATCTCCGTGCT 58.963 55.000 0.00 0.00 0.00 4.40
3458 4295 1.410882 GCTTCCTCTATCTCCGTGCTT 59.589 52.381 0.00 0.00 0.00 3.91
3459 4296 2.544903 GCTTCCTCTATCTCCGTGCTTC 60.545 54.545 0.00 0.00 0.00 3.86
3460 4297 2.437085 TCCTCTATCTCCGTGCTTCA 57.563 50.000 0.00 0.00 0.00 3.02
3461 4298 2.735151 TCCTCTATCTCCGTGCTTCAA 58.265 47.619 0.00 0.00 0.00 2.69
3462 4299 2.427453 TCCTCTATCTCCGTGCTTCAAC 59.573 50.000 0.00 0.00 0.00 3.18
3463 4300 2.428890 CCTCTATCTCCGTGCTTCAACT 59.571 50.000 0.00 0.00 0.00 3.16
3464 4301 3.118956 CCTCTATCTCCGTGCTTCAACTT 60.119 47.826 0.00 0.00 0.00 2.66
3465 4302 4.499183 CTCTATCTCCGTGCTTCAACTTT 58.501 43.478 0.00 0.00 0.00 2.66
3466 4303 4.245660 TCTATCTCCGTGCTTCAACTTTG 58.754 43.478 0.00 0.00 0.00 2.77
3467 4304 2.613026 TCTCCGTGCTTCAACTTTGA 57.387 45.000 0.00 0.00 34.92 2.69
3468 4305 2.210116 TCTCCGTGCTTCAACTTTGAC 58.790 47.619 0.00 0.00 36.83 3.18
3469 4306 1.264288 CTCCGTGCTTCAACTTTGACC 59.736 52.381 0.00 0.00 36.83 4.02
3470 4307 0.041312 CCGTGCTTCAACTTTGACCG 60.041 55.000 0.00 0.00 36.83 4.79
3471 4308 0.655733 CGTGCTTCAACTTTGACCGT 59.344 50.000 0.00 0.00 36.83 4.83
3472 4309 1.862201 CGTGCTTCAACTTTGACCGTA 59.138 47.619 0.00 0.00 36.83 4.02
3473 4310 2.285756 CGTGCTTCAACTTTGACCGTAA 59.714 45.455 0.00 0.00 36.83 3.18
3474 4311 3.242478 CGTGCTTCAACTTTGACCGTAAA 60.242 43.478 0.00 0.00 36.83 2.01
3475 4312 4.553938 CGTGCTTCAACTTTGACCGTAAAT 60.554 41.667 0.00 0.00 36.83 1.40
3476 4313 5.278604 GTGCTTCAACTTTGACCGTAAATT 58.721 37.500 0.00 0.00 36.83 1.82
3477 4314 5.746721 GTGCTTCAACTTTGACCGTAAATTT 59.253 36.000 0.00 0.00 36.83 1.82
3478 4315 6.913673 GTGCTTCAACTTTGACCGTAAATTTA 59.086 34.615 0.00 0.00 36.83 1.40
3479 4316 7.432838 GTGCTTCAACTTTGACCGTAAATTTAA 59.567 33.333 0.00 0.00 36.83 1.52
3480 4317 7.432838 TGCTTCAACTTTGACCGTAAATTTAAC 59.567 33.333 0.00 0.00 36.83 2.01
3481 4318 7.646526 GCTTCAACTTTGACCGTAAATTTAACT 59.353 33.333 0.00 0.00 36.83 2.24
3483 4320 9.934190 TTCAACTTTGACCGTAAATTTAACTAC 57.066 29.630 0.00 0.00 36.83 2.73
3484 4321 8.558700 TCAACTTTGACCGTAAATTTAACTACC 58.441 33.333 0.00 0.00 31.01 3.18
3485 4322 8.344098 CAACTTTGACCGTAAATTTAACTACCA 58.656 33.333 0.00 0.00 0.00 3.25
3486 4323 8.449251 ACTTTGACCGTAAATTTAACTACCAA 57.551 30.769 0.00 0.00 0.00 3.67
3487 4324 8.562052 ACTTTGACCGTAAATTTAACTACCAAG 58.438 33.333 0.00 2.45 0.00 3.61
3488 4325 8.674263 TTTGACCGTAAATTTAACTACCAAGA 57.326 30.769 0.00 0.00 0.00 3.02
3489 4326 7.656707 TGACCGTAAATTTAACTACCAAGAC 57.343 36.000 0.00 0.00 0.00 3.01
3490 4327 6.650390 TGACCGTAAATTTAACTACCAAGACC 59.350 38.462 0.00 0.00 0.00 3.85
3491 4328 5.639082 ACCGTAAATTTAACTACCAAGACCG 59.361 40.000 0.00 0.00 0.00 4.79
3492 4329 5.868801 CCGTAAATTTAACTACCAAGACCGA 59.131 40.000 0.00 0.00 0.00 4.69
3493 4330 6.536224 CCGTAAATTTAACTACCAAGACCGAT 59.464 38.462 0.00 0.00 0.00 4.18
3494 4331 7.064966 CCGTAAATTTAACTACCAAGACCGATT 59.935 37.037 0.00 0.00 0.00 3.34
3495 4332 7.901377 CGTAAATTTAACTACCAAGACCGATTG 59.099 37.037 0.00 0.00 0.00 2.67
3496 4333 5.813080 ATTTAACTACCAAGACCGATTGC 57.187 39.130 0.00 0.00 0.00 3.56
3497 4334 1.722011 AACTACCAAGACCGATTGCG 58.278 50.000 0.00 0.00 37.24 4.85
3522 4359 6.618287 CGGGAGCAAAAATTATATCAGTGA 57.382 37.500 0.00 0.00 0.00 3.41
3523 4360 7.026631 CGGGAGCAAAAATTATATCAGTGAA 57.973 36.000 0.00 0.00 0.00 3.18
3524 4361 7.651808 CGGGAGCAAAAATTATATCAGTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
3525 4362 8.137437 CGGGAGCAAAAATTATATCAGTGAATT 58.863 33.333 0.00 0.00 0.00 2.17
3526 4363 9.468532 GGGAGCAAAAATTATATCAGTGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
3527 4364 9.173939 GGAGCAAAAATTATATCAGTGAATTCG 57.826 33.333 0.00 0.00 0.00 3.34
3528 4365 9.722056 GAGCAAAAATTATATCAGTGAATTCGT 57.278 29.630 0.00 0.00 0.00 3.85
3574 4411 2.517402 TTTTTCACCCGCCGCAGT 60.517 55.556 0.00 0.00 0.00 4.40
3575 4412 2.548295 TTTTTCACCCGCCGCAGTC 61.548 57.895 0.00 0.00 0.00 3.51
3586 4423 2.870161 CGCAGTCGGTCTCGTTCG 60.870 66.667 0.00 0.00 37.69 3.95
3587 4424 2.254651 GCAGTCGGTCTCGTTCGT 59.745 61.111 0.00 0.00 37.69 3.85
3588 4425 1.371389 GCAGTCGGTCTCGTTCGTT 60.371 57.895 0.00 0.00 37.69 3.85
3589 4426 0.110056 GCAGTCGGTCTCGTTCGTTA 60.110 55.000 0.00 0.00 37.69 3.18
3590 4427 1.664016 GCAGTCGGTCTCGTTCGTTAA 60.664 52.381 0.00 0.00 37.69 2.01
3591 4428 2.653890 CAGTCGGTCTCGTTCGTTAAA 58.346 47.619 0.00 0.00 37.69 1.52
3592 4429 3.240069 CAGTCGGTCTCGTTCGTTAAAT 58.760 45.455 0.00 0.00 37.69 1.40
3593 4430 3.671928 CAGTCGGTCTCGTTCGTTAAATT 59.328 43.478 0.00 0.00 37.69 1.82
3594 4431 4.149396 CAGTCGGTCTCGTTCGTTAAATTT 59.851 41.667 0.00 0.00 37.69 1.82
3595 4432 5.343058 CAGTCGGTCTCGTTCGTTAAATTTA 59.657 40.000 0.00 0.00 37.69 1.40
3596 4433 6.034256 CAGTCGGTCTCGTTCGTTAAATTTAT 59.966 38.462 0.00 0.00 37.69 1.40
3597 4434 6.034256 AGTCGGTCTCGTTCGTTAAATTTATG 59.966 38.462 0.00 0.00 37.69 1.90
3598 4435 5.289193 TCGGTCTCGTTCGTTAAATTTATGG 59.711 40.000 0.00 0.00 37.69 2.74
3599 4436 5.062558 CGGTCTCGTTCGTTAAATTTATGGT 59.937 40.000 0.00 0.00 0.00 3.55
3600 4437 6.472680 GGTCTCGTTCGTTAAATTTATGGTC 58.527 40.000 0.00 0.00 0.00 4.02
3601 4438 6.091169 GGTCTCGTTCGTTAAATTTATGGTCA 59.909 38.462 0.00 0.00 0.00 4.02
3602 4439 7.360269 GGTCTCGTTCGTTAAATTTATGGTCAA 60.360 37.037 0.00 0.00 0.00 3.18
3603 4440 8.011106 GTCTCGTTCGTTAAATTTATGGTCAAA 58.989 33.333 0.00 0.00 0.00 2.69
3604 4441 8.225107 TCTCGTTCGTTAAATTTATGGTCAAAG 58.775 33.333 0.00 0.00 0.00 2.77
3605 4442 7.863666 TCGTTCGTTAAATTTATGGTCAAAGT 58.136 30.769 0.00 0.00 0.00 2.66
3606 4443 8.344098 TCGTTCGTTAAATTTATGGTCAAAGTT 58.656 29.630 0.00 0.00 31.36 2.66
3607 4444 8.624028 CGTTCGTTAAATTTATGGTCAAAGTTC 58.376 33.333 0.00 0.00 29.44 3.01
3608 4445 8.624028 GTTCGTTAAATTTATGGTCAAAGTTCG 58.376 33.333 0.00 0.00 29.44 3.95
3609 4446 8.085720 TCGTTAAATTTATGGTCAAAGTTCGA 57.914 30.769 0.00 0.00 29.44 3.71
3610 4447 8.011106 TCGTTAAATTTATGGTCAAAGTTCGAC 58.989 33.333 0.00 0.00 29.44 4.20
3616 4453 2.823628 GTCAAAGTTCGACCTCGGG 58.176 57.895 0.00 0.00 40.29 5.14
3617 4454 0.316204 GTCAAAGTTCGACCTCGGGA 59.684 55.000 0.00 0.00 40.29 5.14
3618 4455 1.042229 TCAAAGTTCGACCTCGGGAA 58.958 50.000 0.00 0.00 40.29 3.97
3619 4456 1.000506 TCAAAGTTCGACCTCGGGAAG 59.999 52.381 0.00 0.00 40.29 3.46
3620 4457 0.320508 AAAGTTCGACCTCGGGAAGC 60.321 55.000 0.00 0.00 40.29 3.86
3621 4458 2.488087 AAGTTCGACCTCGGGAAGCG 62.488 60.000 0.00 0.00 40.29 4.68
3622 4459 4.430765 TTCGACCTCGGGAAGCGC 62.431 66.667 0.00 0.00 40.29 5.92
3625 4462 3.760035 GACCTCGGGAAGCGCAGA 61.760 66.667 11.47 0.00 0.00 4.26
3626 4463 3.991536 GACCTCGGGAAGCGCAGAC 62.992 68.421 11.47 0.00 0.00 3.51
3640 4477 3.238903 CGCAGACGCACTATATTTTGG 57.761 47.619 0.00 0.00 38.40 3.28
3641 4478 2.863740 CGCAGACGCACTATATTTTGGA 59.136 45.455 0.00 0.00 38.40 3.53
3642 4479 3.308595 CGCAGACGCACTATATTTTGGAA 59.691 43.478 0.00 0.00 38.40 3.53
3643 4480 4.024893 CGCAGACGCACTATATTTTGGAAT 60.025 41.667 0.00 0.00 38.40 3.01
3644 4481 5.207768 GCAGACGCACTATATTTTGGAATG 58.792 41.667 0.00 0.00 38.36 2.67
3645 4482 5.751680 CAGACGCACTATATTTTGGAATGG 58.248 41.667 0.00 0.00 0.00 3.16
3646 4483 5.527214 CAGACGCACTATATTTTGGAATGGA 59.473 40.000 0.00 0.00 0.00 3.41
3647 4484 5.760253 AGACGCACTATATTTTGGAATGGAG 59.240 40.000 0.00 0.00 0.00 3.86
3648 4485 4.821805 ACGCACTATATTTTGGAATGGAGG 59.178 41.667 0.00 0.00 0.00 4.30
3649 4486 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
3650 4487 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
3651 4488 5.474876 GCACTATATTTTGGAATGGAGGGAG 59.525 44.000 0.00 0.00 0.00 4.30
3652 4489 6.605119 CACTATATTTTGGAATGGAGGGAGT 58.395 40.000 0.00 0.00 0.00 3.85
3653 4490 7.691791 GCACTATATTTTGGAATGGAGGGAGTA 60.692 40.741 0.00 0.00 0.00 2.59
3666 4503 8.401955 AATGGAGGGAGTAGGTTAAGATTTTA 57.598 34.615 0.00 0.00 0.00 1.52
3667 4504 7.433537 TGGAGGGAGTAGGTTAAGATTTTAG 57.566 40.000 0.00 0.00 0.00 1.85
3668 4505 6.964086 TGGAGGGAGTAGGTTAAGATTTTAGT 59.036 38.462 0.00 0.00 0.00 2.24
3684 4521 2.217510 TAGTTCTCTCAGGGCGAAGT 57.782 50.000 0.00 0.00 0.00 3.01
3685 4522 1.343069 AGTTCTCTCAGGGCGAAGTT 58.657 50.000 0.00 0.00 0.00 2.66
3690 4527 0.456221 TCTCAGGGCGAAGTTCGATC 59.544 55.000 28.66 18.03 43.74 3.69
3691 4528 0.867753 CTCAGGGCGAAGTTCGATCG 60.868 60.000 28.66 9.36 43.74 3.69
3692 4529 1.138883 CAGGGCGAAGTTCGATCGA 59.861 57.895 28.66 15.15 43.74 3.59
3693 4530 0.457853 CAGGGCGAAGTTCGATCGAA 60.458 55.000 28.66 25.96 43.74 3.71
3694 4531 0.460311 AGGGCGAAGTTCGATCGAAT 59.540 50.000 31.24 18.10 43.74 3.34
3695 4532 0.577269 GGGCGAAGTTCGATCGAATG 59.423 55.000 31.24 21.44 43.74 2.67
3696 4533 1.556564 GGCGAAGTTCGATCGAATGA 58.443 50.000 31.24 8.96 43.74 2.57
3697 4534 1.255600 GGCGAAGTTCGATCGAATGAC 59.744 52.381 31.24 20.36 43.74 3.06
3698 4535 1.917955 GCGAAGTTCGATCGAATGACA 59.082 47.619 31.24 8.15 43.74 3.58
3700 4537 2.035342 CGAAGTTCGATCGAATGACAGC 60.035 50.000 31.24 18.00 43.74 4.40
3701 4538 1.550065 AGTTCGATCGAATGACAGCG 58.450 50.000 31.24 0.00 36.45 5.18
3702 4539 0.043822 GTTCGATCGAATGACAGCGC 60.044 55.000 31.24 13.60 36.45 5.92
3747 4584 5.278512 GGACTTGTCCTCCTCAAATTTGTTC 60.279 44.000 17.47 3.44 0.00 3.18
3755 4592 2.147958 CTCAAATTTGTTCGTCGGGGA 58.852 47.619 17.47 0.00 0.00 4.81
3762 4599 2.953466 TGTTCGTCGGGGAAGATTAG 57.047 50.000 0.00 0.00 0.00 1.73
3764 4601 2.165030 TGTTCGTCGGGGAAGATTAGAC 59.835 50.000 0.00 0.00 0.00 2.59
3769 4606 2.362717 GTCGGGGAAGATTAGACAGAGG 59.637 54.545 0.00 0.00 32.57 3.69
3794 4631 3.878103 TCACGTAGACTCTTATCAGCTCC 59.122 47.826 0.00 0.00 0.00 4.70
3795 4632 3.628032 CACGTAGACTCTTATCAGCTCCA 59.372 47.826 0.00 0.00 0.00 3.86
3799 4636 5.240623 CGTAGACTCTTATCAGCTCCAAGAT 59.759 44.000 2.52 0.00 0.00 2.40
3812 4649 5.526846 CAGCTCCAAGATGTTAGGATTTCTC 59.473 44.000 0.00 0.00 0.00 2.87
3816 4653 5.250543 TCCAAGATGTTAGGATTTCTCACCA 59.749 40.000 0.00 0.00 0.00 4.17
3826 4663 1.378531 TTTCTCACCATGCGTATGCC 58.621 50.000 8.12 0.00 41.78 4.40
3827 4664 0.251634 TTCTCACCATGCGTATGCCA 59.748 50.000 8.12 0.00 41.78 4.92
3853 4690 3.315191 CCAGATTTGGTGTCACGTTCTTT 59.685 43.478 0.00 0.00 39.79 2.52
3873 4710 5.889853 TCTTTGGATCAATTCAAGGGATCAG 59.110 40.000 0.00 0.00 39.30 2.90
3874 4711 3.559069 TGGATCAATTCAAGGGATCAGC 58.441 45.455 0.00 0.00 39.30 4.26
3875 4712 3.053470 TGGATCAATTCAAGGGATCAGCA 60.053 43.478 0.00 0.00 39.30 4.41
3876 4713 3.568853 GGATCAATTCAAGGGATCAGCAG 59.431 47.826 0.00 0.00 39.30 4.24
3877 4714 2.372264 TCAATTCAAGGGATCAGCAGC 58.628 47.619 0.00 0.00 0.00 5.25
3878 4715 1.065102 CAATTCAAGGGATCAGCAGCG 59.935 52.381 0.00 0.00 0.00 5.18
3879 4716 0.543277 ATTCAAGGGATCAGCAGCGA 59.457 50.000 0.00 0.00 0.00 4.93
3880 4717 0.391661 TTCAAGGGATCAGCAGCGAC 60.392 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 3.808771 ATCGTCTCGATCGGCACGC 62.809 63.158 25.56 9.44 43.45 5.34
85 86 2.006062 CATCGTCTCGATCGGCACG 61.006 63.158 24.85 24.85 46.43 5.34
86 87 0.039978 ATCATCGTCTCGATCGGCAC 60.040 55.000 16.41 11.00 45.19 5.01
128 129 1.012486 GTGGTGCGGCACTAGTGTAC 61.012 60.000 29.92 15.58 34.40 2.90
336 342 4.556942 TCAGATGCCGCTGAAATATTTG 57.443 40.909 5.17 0.00 41.65 2.32
347 353 2.939103 AGTCAGTAATTTCAGATGCCGC 59.061 45.455 0.00 0.00 0.00 6.53
384 390 2.618794 TGGTCCTTTGGCCAAAATGAT 58.381 42.857 29.93 0.00 0.00 2.45
410 416 6.816134 TTGTTTGATCTCAATCCAATCGAA 57.184 33.333 0.00 0.00 35.55 3.71
510 517 7.848051 GTGCATACTGAAATATTCGTCTTTCTG 59.152 37.037 0.00 0.00 36.77 3.02
515 522 4.745125 CGGTGCATACTGAAATATTCGTCT 59.255 41.667 0.00 0.00 35.05 4.18
532 539 6.078202 TGAAAATTCAGTAATTTCGGTGCA 57.922 33.333 0.00 0.00 43.04 4.57
559 566 3.154827 TCCCATGGTCTTCACCTTTTC 57.845 47.619 11.73 0.00 44.17 2.29
683 690 1.065998 TCCGGTAAAGGGAAATCACGG 60.066 52.381 0.00 0.00 41.28 4.94
696 703 3.215151 TGTGCACTCATTTTTCCGGTAA 58.785 40.909 19.41 0.00 0.00 2.85
699 706 3.302365 AATGTGCACTCATTTTTCCGG 57.698 42.857 19.41 0.00 34.86 5.14
702 709 6.586868 TTGACAAATGTGCACTCATTTTTC 57.413 33.333 19.41 17.47 42.88 2.29
729 737 5.049680 CGGCAGAGACTTAGAGAGAGAATAC 60.050 48.000 0.00 0.00 0.00 1.89
780 788 1.108727 TGCTTTGGTTGAGTGGGCTG 61.109 55.000 0.00 0.00 0.00 4.85
826 835 2.414161 GGGTTAATCTGTTCTTGTGCGC 60.414 50.000 0.00 0.00 0.00 6.09
888 1664 6.118170 AGTACTACTGCTATCTTGGTCGTAA 58.882 40.000 0.00 0.00 0.00 3.18
889 1665 5.678583 AGTACTACTGCTATCTTGGTCGTA 58.321 41.667 0.00 0.00 0.00 3.43
890 1666 4.525024 AGTACTACTGCTATCTTGGTCGT 58.475 43.478 0.00 0.00 0.00 4.34
903 1682 5.892160 TTGGTGCTGTACTAGTACTACTG 57.108 43.478 28.56 18.16 41.25 2.74
905 1684 5.860716 GTGTTTGGTGCTGTACTAGTACTAC 59.139 44.000 28.56 23.07 41.25 2.73
1077 1868 1.683790 CGAACCACGGCGTGAAGATC 61.684 60.000 38.91 26.50 35.23 2.75
1164 1955 1.944676 GCCGAAGATGTAGGTCGCG 60.945 63.158 0.00 0.00 33.46 5.87
1193 1984 2.876645 GCGAGGACTTGAGCGTCG 60.877 66.667 0.00 0.00 43.92 5.12
1291 2082 2.805353 CGGCGTGACCTCGTTGAG 60.805 66.667 0.00 0.00 35.61 3.02
1332 2123 1.003839 GACGAGGTTCATGGTGGCA 60.004 57.895 0.00 0.00 0.00 4.92
2571 3401 2.749044 TCGGCGTCGTAGAGCCTT 60.749 61.111 10.18 0.00 44.62 4.35
2938 3768 1.142748 CTCCACCTCATGAGTCGCC 59.857 63.158 21.11 0.00 0.00 5.54
3022 3859 7.548196 TCAAGATGAAGAAAAAGTAACACGT 57.452 32.000 0.00 0.00 0.00 4.49
3023 3860 6.575201 GCTCAAGATGAAGAAAAAGTAACACG 59.425 38.462 0.00 0.00 0.00 4.49
3039 3876 3.129462 TCTCCTTACTGTCGCTCAAGATG 59.871 47.826 0.00 0.00 0.00 2.90
3040 3877 3.357203 TCTCCTTACTGTCGCTCAAGAT 58.643 45.455 0.00 0.00 0.00 2.40
3100 3937 2.758089 GCGACGGCGTCCTTCTCTA 61.758 63.158 31.86 0.00 40.36 2.43
3162 3999 2.589890 GACGTGTGTCAGTGACCAC 58.410 57.895 23.96 23.96 44.82 4.16
3211 4048 1.375523 GGGTCAATGACGCGTTCCT 60.376 57.895 15.53 0.00 35.92 3.36
3269 4106 3.181329 TCAATCTCCTTGCAAGAGGGTA 58.819 45.455 28.05 8.53 37.41 3.69
3293 4130 7.362056 CGAAGATCAAGGGAAGAAATGCTTTTA 60.362 37.037 0.00 0.00 36.83 1.52
3298 4135 3.691609 ACGAAGATCAAGGGAAGAAATGC 59.308 43.478 0.00 0.00 0.00 3.56
3303 4140 3.056536 CACTGACGAAGATCAAGGGAAGA 60.057 47.826 0.00 0.00 0.00 2.87
3318 4155 2.266554 GAATTCAGGAGCTCACTGACG 58.733 52.381 25.45 7.67 44.07 4.35
3391 4228 0.393402 TACTAGCCGAAGCCGAGACA 60.393 55.000 0.00 0.00 41.25 3.41
3392 4229 0.308376 CTACTAGCCGAAGCCGAGAC 59.692 60.000 0.00 0.00 41.25 3.36
3415 4252 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
3416 4253 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
3420 4257 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
3421 4258 3.129287 GGAAGCACTACATTGTGGAATGG 59.871 47.826 7.20 0.00 43.00 3.16
3422 4259 4.012374 AGGAAGCACTACATTGTGGAATG 58.988 43.478 7.20 0.00 44.11 2.67
3423 4260 4.018960 AGAGGAAGCACTACATTGTGGAAT 60.019 41.667 7.20 0.00 38.31 3.01
3424 4261 3.327757 AGAGGAAGCACTACATTGTGGAA 59.672 43.478 7.20 0.00 38.31 3.53
3425 4262 2.906389 AGAGGAAGCACTACATTGTGGA 59.094 45.455 7.20 0.00 38.31 4.02
3426 4263 3.340814 AGAGGAAGCACTACATTGTGG 57.659 47.619 0.00 0.00 38.31 4.17
3427 4264 5.911752 AGATAGAGGAAGCACTACATTGTG 58.088 41.667 0.00 0.00 40.62 3.33
3428 4265 5.069781 GGAGATAGAGGAAGCACTACATTGT 59.930 44.000 0.00 0.00 0.00 2.71
3429 4266 5.537188 GGAGATAGAGGAAGCACTACATTG 58.463 45.833 0.00 0.00 0.00 2.82
3430 4267 4.279671 CGGAGATAGAGGAAGCACTACATT 59.720 45.833 0.00 0.00 0.00 2.71
3431 4268 3.823873 CGGAGATAGAGGAAGCACTACAT 59.176 47.826 0.00 0.00 0.00 2.29
3432 4269 3.215151 CGGAGATAGAGGAAGCACTACA 58.785 50.000 0.00 0.00 0.00 2.74
3433 4270 3.003897 CACGGAGATAGAGGAAGCACTAC 59.996 52.174 0.00 0.00 0.00 2.73
3434 4271 3.215151 CACGGAGATAGAGGAAGCACTA 58.785 50.000 0.00 0.00 0.00 2.74
3435 4272 2.028130 CACGGAGATAGAGGAAGCACT 58.972 52.381 0.00 0.00 0.00 4.40
3436 4273 1.537135 GCACGGAGATAGAGGAAGCAC 60.537 57.143 0.00 0.00 0.00 4.40
3437 4274 0.747255 GCACGGAGATAGAGGAAGCA 59.253 55.000 0.00 0.00 0.00 3.91
3438 4275 1.036707 AGCACGGAGATAGAGGAAGC 58.963 55.000 0.00 0.00 0.00 3.86
3439 4276 2.690497 TGAAGCACGGAGATAGAGGAAG 59.310 50.000 0.00 0.00 0.00 3.46
3440 4277 2.735151 TGAAGCACGGAGATAGAGGAA 58.265 47.619 0.00 0.00 0.00 3.36
3441 4278 2.427453 GTTGAAGCACGGAGATAGAGGA 59.573 50.000 0.00 0.00 0.00 3.71
3442 4279 2.428890 AGTTGAAGCACGGAGATAGAGG 59.571 50.000 0.00 0.00 0.00 3.69
3443 4280 3.791973 AGTTGAAGCACGGAGATAGAG 57.208 47.619 0.00 0.00 0.00 2.43
3444 4281 4.021456 TCAAAGTTGAAGCACGGAGATAGA 60.021 41.667 0.00 0.00 33.55 1.98
3445 4282 4.092091 GTCAAAGTTGAAGCACGGAGATAG 59.908 45.833 0.00 0.00 39.21 2.08
3446 4283 3.994392 GTCAAAGTTGAAGCACGGAGATA 59.006 43.478 0.00 0.00 39.21 1.98
3447 4284 2.808543 GTCAAAGTTGAAGCACGGAGAT 59.191 45.455 0.00 0.00 39.21 2.75
3448 4285 2.210116 GTCAAAGTTGAAGCACGGAGA 58.790 47.619 0.00 0.00 39.21 3.71
3449 4286 1.264288 GGTCAAAGTTGAAGCACGGAG 59.736 52.381 0.00 0.00 39.21 4.63
3450 4287 1.305201 GGTCAAAGTTGAAGCACGGA 58.695 50.000 0.00 0.00 39.21 4.69
3451 4288 0.041312 CGGTCAAAGTTGAAGCACGG 60.041 55.000 0.00 0.00 39.21 4.94
3452 4289 0.655733 ACGGTCAAAGTTGAAGCACG 59.344 50.000 0.00 2.00 39.21 5.34
3453 4290 3.955771 TTACGGTCAAAGTTGAAGCAC 57.044 42.857 0.00 0.00 39.21 4.40
3454 4291 5.508200 AATTTACGGTCAAAGTTGAAGCA 57.492 34.783 0.00 0.00 39.21 3.91
3455 4292 7.646526 AGTTAAATTTACGGTCAAAGTTGAAGC 59.353 33.333 0.00 0.00 39.21 3.86
3457 4294 9.934190 GTAGTTAAATTTACGGTCAAAGTTGAA 57.066 29.630 0.00 0.00 39.21 2.69
3458 4295 8.558700 GGTAGTTAAATTTACGGTCAAAGTTGA 58.441 33.333 0.00 0.00 34.20 3.18
3459 4296 8.344098 TGGTAGTTAAATTTACGGTCAAAGTTG 58.656 33.333 0.00 0.00 29.44 3.16
3460 4297 8.449251 TGGTAGTTAAATTTACGGTCAAAGTT 57.551 30.769 0.00 0.00 31.36 2.66
3461 4298 8.449251 TTGGTAGTTAAATTTACGGTCAAAGT 57.551 30.769 0.00 0.00 0.00 2.66
3462 4299 8.776470 TCTTGGTAGTTAAATTTACGGTCAAAG 58.224 33.333 0.00 0.00 0.00 2.77
3463 4300 8.558700 GTCTTGGTAGTTAAATTTACGGTCAAA 58.441 33.333 0.00 0.00 0.00 2.69
3464 4301 7.173047 GGTCTTGGTAGTTAAATTTACGGTCAA 59.827 37.037 0.00 0.00 0.00 3.18
3465 4302 6.650390 GGTCTTGGTAGTTAAATTTACGGTCA 59.350 38.462 0.00 0.00 0.00 4.02
3466 4303 6.183360 CGGTCTTGGTAGTTAAATTTACGGTC 60.183 42.308 0.00 0.00 0.00 4.79
3467 4304 5.639082 CGGTCTTGGTAGTTAAATTTACGGT 59.361 40.000 0.00 0.00 0.00 4.83
3468 4305 5.868801 TCGGTCTTGGTAGTTAAATTTACGG 59.131 40.000 0.00 0.00 0.00 4.02
3469 4306 6.949578 TCGGTCTTGGTAGTTAAATTTACG 57.050 37.500 0.00 0.00 0.00 3.18
3470 4307 7.695201 GCAATCGGTCTTGGTAGTTAAATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
3471 4308 7.413219 CGCAATCGGTCTTGGTAGTTAAATTTA 60.413 37.037 0.00 0.00 0.00 1.40
3472 4309 6.617879 GCAATCGGTCTTGGTAGTTAAATTT 58.382 36.000 0.00 0.00 0.00 1.82
3473 4310 5.163794 CGCAATCGGTCTTGGTAGTTAAATT 60.164 40.000 0.00 0.00 0.00 1.82
3474 4311 4.331717 CGCAATCGGTCTTGGTAGTTAAAT 59.668 41.667 0.00 0.00 0.00 1.40
3475 4312 3.680937 CGCAATCGGTCTTGGTAGTTAAA 59.319 43.478 0.00 0.00 0.00 1.52
3476 4313 3.255725 CGCAATCGGTCTTGGTAGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
3477 4314 2.883574 CGCAATCGGTCTTGGTAGTTA 58.116 47.619 0.00 0.00 0.00 2.24
3478 4315 1.722011 CGCAATCGGTCTTGGTAGTT 58.278 50.000 0.00 0.00 0.00 2.24
3479 4316 3.436001 CGCAATCGGTCTTGGTAGT 57.564 52.632 0.00 0.00 0.00 2.73
3491 4328 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
3492 4329 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
3493 4330 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
3494 4331 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
3495 4332 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
3496 4333 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
3497 4334 4.278419 ACTGATATAATTTTTGCTCCCGCC 59.722 41.667 0.00 0.00 34.43 6.13
3498 4335 5.008613 TCACTGATATAATTTTTGCTCCCGC 59.991 40.000 0.00 0.00 0.00 6.13
3499 4336 6.618287 TCACTGATATAATTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
3500 4337 9.468532 GAATTCACTGATATAATTTTTGCTCCC 57.531 33.333 0.00 0.00 0.00 4.30
3501 4338 9.173939 CGAATTCACTGATATAATTTTTGCTCC 57.826 33.333 6.22 0.00 0.00 4.70
3502 4339 9.722056 ACGAATTCACTGATATAATTTTTGCTC 57.278 29.630 6.22 0.00 0.00 4.26
3557 4394 2.517402 ACTGCGGCGGGTGAAAAA 60.517 55.556 14.26 0.00 0.00 1.94
3558 4395 2.975799 GACTGCGGCGGGTGAAAA 60.976 61.111 14.26 0.00 0.00 2.29
3569 4406 2.870161 CGAACGAGACCGACTGCG 60.870 66.667 0.00 0.00 39.50 5.18
3570 4407 0.110056 TAACGAACGAGACCGACTGC 60.110 55.000 0.14 0.00 39.50 4.40
3571 4408 2.320805 TTAACGAACGAGACCGACTG 57.679 50.000 0.14 0.00 39.50 3.51
3572 4409 3.565905 ATTTAACGAACGAGACCGACT 57.434 42.857 0.14 0.00 39.50 4.18
3573 4410 4.635961 AAATTTAACGAACGAGACCGAC 57.364 40.909 0.14 0.00 39.50 4.79
3574 4411 5.289193 CCATAAATTTAACGAACGAGACCGA 59.711 40.000 1.21 0.00 39.50 4.69
3575 4412 5.062558 ACCATAAATTTAACGAACGAGACCG 59.937 40.000 1.21 0.00 42.50 4.79
3576 4413 6.091169 TGACCATAAATTTAACGAACGAGACC 59.909 38.462 1.21 0.00 0.00 3.85
3577 4414 7.052565 TGACCATAAATTTAACGAACGAGAC 57.947 36.000 1.21 0.00 0.00 3.36
3578 4415 7.655236 TTGACCATAAATTTAACGAACGAGA 57.345 32.000 1.21 0.00 0.00 4.04
3579 4416 8.013378 ACTTTGACCATAAATTTAACGAACGAG 58.987 33.333 1.21 0.01 0.00 4.18
3580 4417 7.863666 ACTTTGACCATAAATTTAACGAACGA 58.136 30.769 1.21 0.00 0.00 3.85
3581 4418 8.496872 AACTTTGACCATAAATTTAACGAACG 57.503 30.769 1.21 0.00 0.00 3.95
3582 4419 8.624028 CGAACTTTGACCATAAATTTAACGAAC 58.376 33.333 1.21 0.00 0.00 3.95
3583 4420 8.557864 TCGAACTTTGACCATAAATTTAACGAA 58.442 29.630 1.21 1.12 0.00 3.85
3584 4421 8.011106 GTCGAACTTTGACCATAAATTTAACGA 58.989 33.333 1.21 0.00 0.00 3.85
3585 4422 8.142348 GTCGAACTTTGACCATAAATTTAACG 57.858 34.615 1.21 0.00 0.00 3.18
3598 4435 0.316204 TCCCGAGGTCGAACTTTGAC 59.684 55.000 3.47 0.86 43.02 3.18
3599 4436 1.000506 CTTCCCGAGGTCGAACTTTGA 59.999 52.381 3.47 0.00 43.02 2.69
3600 4437 1.429463 CTTCCCGAGGTCGAACTTTG 58.571 55.000 3.47 0.00 43.02 2.77
3601 4438 0.320508 GCTTCCCGAGGTCGAACTTT 60.321 55.000 3.47 0.00 43.02 2.66
3602 4439 1.292541 GCTTCCCGAGGTCGAACTT 59.707 57.895 3.47 0.00 43.02 2.66
3603 4440 2.971452 GCTTCCCGAGGTCGAACT 59.029 61.111 0.34 0.34 43.02 3.01
3604 4441 2.506438 CGCTTCCCGAGGTCGAAC 60.506 66.667 0.00 0.00 43.02 3.95
3605 4442 4.430765 GCGCTTCCCGAGGTCGAA 62.431 66.667 0.00 0.00 43.02 3.71
3608 4445 3.760035 TCTGCGCTTCCCGAGGTC 61.760 66.667 9.73 0.00 40.02 3.85
3609 4446 4.070552 GTCTGCGCTTCCCGAGGT 62.071 66.667 9.73 0.00 40.02 3.85
3621 4458 4.875544 TTCCAAAATATAGTGCGTCTGC 57.124 40.909 0.00 0.00 43.20 4.26
3622 4459 5.527214 TCCATTCCAAAATATAGTGCGTCTG 59.473 40.000 0.00 0.00 0.00 3.51
3623 4460 5.680619 TCCATTCCAAAATATAGTGCGTCT 58.319 37.500 0.00 0.00 0.00 4.18
3624 4461 5.049405 CCTCCATTCCAAAATATAGTGCGTC 60.049 44.000 0.00 0.00 0.00 5.19
3625 4462 4.821805 CCTCCATTCCAAAATATAGTGCGT 59.178 41.667 0.00 0.00 0.00 5.24
3626 4463 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
3627 4464 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
3628 4465 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
3629 4466 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
3630 4467 7.017651 ACCTACTCCCTCCATTCCAAAATATAG 59.982 40.741 0.00 0.00 0.00 1.31
3631 4468 6.855061 ACCTACTCCCTCCATTCCAAAATATA 59.145 38.462 0.00 0.00 0.00 0.86
3632 4469 5.676811 ACCTACTCCCTCCATTCCAAAATAT 59.323 40.000 0.00 0.00 0.00 1.28
3633 4470 5.043762 ACCTACTCCCTCCATTCCAAAATA 58.956 41.667 0.00 0.00 0.00 1.40
3634 4471 3.858638 ACCTACTCCCTCCATTCCAAAAT 59.141 43.478 0.00 0.00 0.00 1.82
3635 4472 3.265489 ACCTACTCCCTCCATTCCAAAA 58.735 45.455 0.00 0.00 0.00 2.44
3636 4473 2.929301 ACCTACTCCCTCCATTCCAAA 58.071 47.619 0.00 0.00 0.00 3.28
3637 4474 2.661176 ACCTACTCCCTCCATTCCAA 57.339 50.000 0.00 0.00 0.00 3.53
3638 4475 2.661176 AACCTACTCCCTCCATTCCA 57.339 50.000 0.00 0.00 0.00 3.53
3639 4476 4.296056 TCTTAACCTACTCCCTCCATTCC 58.704 47.826 0.00 0.00 0.00 3.01
3640 4477 6.502074 AATCTTAACCTACTCCCTCCATTC 57.498 41.667 0.00 0.00 0.00 2.67
3641 4478 6.910259 AAATCTTAACCTACTCCCTCCATT 57.090 37.500 0.00 0.00 0.00 3.16
3642 4479 6.910259 AAAATCTTAACCTACTCCCTCCAT 57.090 37.500 0.00 0.00 0.00 3.41
3643 4480 6.964086 ACTAAAATCTTAACCTACTCCCTCCA 59.036 38.462 0.00 0.00 0.00 3.86
3644 4481 7.434927 ACTAAAATCTTAACCTACTCCCTCC 57.565 40.000 0.00 0.00 0.00 4.30
3645 4482 8.760735 AGAACTAAAATCTTAACCTACTCCCTC 58.239 37.037 0.00 0.00 0.00 4.30
3646 4483 8.682297 AGAACTAAAATCTTAACCTACTCCCT 57.318 34.615 0.00 0.00 0.00 4.20
3647 4484 8.760735 AGAGAACTAAAATCTTAACCTACTCCC 58.239 37.037 0.00 0.00 0.00 4.30
3648 4485 9.806203 GAGAGAACTAAAATCTTAACCTACTCC 57.194 37.037 0.00 0.00 0.00 3.85
3651 4488 9.589111 CCTGAGAGAACTAAAATCTTAACCTAC 57.411 37.037 0.00 0.00 0.00 3.18
3652 4489 8.759782 CCCTGAGAGAACTAAAATCTTAACCTA 58.240 37.037 0.00 0.00 0.00 3.08
3653 4490 7.625469 CCCTGAGAGAACTAAAATCTTAACCT 58.375 38.462 0.00 0.00 0.00 3.50
3666 4503 1.273886 GAACTTCGCCCTGAGAGAACT 59.726 52.381 0.00 0.00 0.00 3.01
3667 4504 1.715993 GAACTTCGCCCTGAGAGAAC 58.284 55.000 0.00 0.00 0.00 3.01
3668 4505 0.243907 CGAACTTCGCCCTGAGAGAA 59.756 55.000 0.00 0.00 31.14 2.87
3676 4513 0.577269 CATTCGATCGAACTTCGCCC 59.423 55.000 31.27 0.18 40.21 6.13
3684 4521 0.179137 AGCGCTGTCATTCGATCGAA 60.179 50.000 30.83 30.83 38.59 3.71
3685 4522 0.179137 AAGCGCTGTCATTCGATCGA 60.179 50.000 15.15 15.15 0.00 3.59
3747 4584 2.022195 TCTGTCTAATCTTCCCCGACG 58.978 52.381 0.00 0.00 0.00 5.12
3773 4610 3.628032 TGGAGCTGATAAGAGTCTACGTG 59.372 47.826 0.00 0.00 0.00 4.49
3781 4618 6.041409 TCCTAACATCTTGGAGCTGATAAGAG 59.959 42.308 0.00 0.00 34.30 2.85
3786 4623 5.643421 AATCCTAACATCTTGGAGCTGAT 57.357 39.130 0.00 0.00 32.95 2.90
3794 4631 6.459298 GCATGGTGAGAAATCCTAACATCTTG 60.459 42.308 0.00 0.00 0.00 3.02
3795 4632 5.591877 GCATGGTGAGAAATCCTAACATCTT 59.408 40.000 0.00 0.00 0.00 2.40
3799 4636 3.270027 CGCATGGTGAGAAATCCTAACA 58.730 45.455 0.00 0.00 0.00 2.41
3812 4649 2.822758 CGGTGGCATACGCATGGTG 61.823 63.158 0.00 0.00 41.24 4.17
3832 4669 4.282068 CAAAGAACGTGACACCAAATCTG 58.718 43.478 0.00 0.00 0.00 2.90
3842 4679 5.356882 TGAATTGATCCAAAGAACGTGAC 57.643 39.130 0.00 0.00 0.00 3.67
3853 4690 3.053470 TGCTGATCCCTTGAATTGATCCA 60.053 43.478 0.00 0.00 35.18 3.41


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

AutoCloner maintained by Alex Coulton.