Multiple sequence alignment - TraesCS6D01G240100

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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 TraesCS6D01G240100 chr6D 100.000 6106 0 0 1 6106 341193264 341199369 0.000000e+00 11276.0
1 TraesCS6D01G240100 chr6A 96.005 1752 48 6 724 2457 481255515 481257262 0.000000e+00 2828.0
2 TraesCS6D01G240100 chr6A 92.396 1828 90 25 3523 5332 481258339 481260135 0.000000e+00 2560.0
3 TraesCS6D01G240100 chr6A 94.404 554 26 3 2717 3267 481257578 481258129 0.000000e+00 846.0
4 TraesCS6D01G240100 chr6B 95.475 1746 53 8 728 2457 479083541 479081806 0.000000e+00 2763.0
5 TraesCS6D01G240100 chr6B 96.131 1008 27 6 4255 5262 479079822 479078827 0.000000e+00 1635.0
6 TraesCS6D01G240100 chr6B 91.753 679 44 6 3526 4200 479080577 479079907 0.000000e+00 933.0
7 TraesCS6D01G240100 chr6B 88.515 653 26 10 2664 3277 479081606 479080964 0.000000e+00 745.0
8 TraesCS6D01G240100 chr6B 85.096 208 28 3 5334 5539 218229768 218229562 6.200000e-50 209.0
9 TraesCS6D01G240100 chr6B 93.878 49 3 0 6041 6089 479078427 479078379 2.360000e-09 75.0
10 TraesCS6D01G240100 chr7A 95.592 726 32 0 1 726 731881336 731880611 0.000000e+00 1164.0
11 TraesCS6D01G240100 chr7A 87.586 725 89 1 2 726 579091643 579092366 0.000000e+00 839.0
12 TraesCS6D01G240100 chr5D 93.908 673 27 4 5334 5999 332370661 332369996 0.000000e+00 1003.0
13 TraesCS6D01G240100 chr4A 93.462 673 37 3 5334 5999 627605000 627604328 0.000000e+00 992.0
14 TraesCS6D01G240100 chr4A 84.409 186 23 6 5334 5515 321899573 321899390 1.750000e-40 178.0
15 TraesCS6D01G240100 chr7B 93.953 645 30 5 5362 5999 634169187 634169829 0.000000e+00 966.0
16 TraesCS6D01G240100 chr7B 83.104 728 119 4 1 726 556496866 556496141 0.000000e+00 660.0
17 TraesCS6D01G240100 chr1B 91.147 689 34 7 5335 5999 662037207 662036522 0.000000e+00 909.0
18 TraesCS6D01G240100 chr1B 94.286 35 2 0 4418 4452 603263079 603263113 3.000000e-03 54.7
19 TraesCS6D01G240100 chr2D 86.630 733 93 2 1 733 14716857 14717584 0.000000e+00 806.0
20 TraesCS6D01G240100 chr2D 83.099 213 28 8 5334 5541 81159494 81159703 2.910000e-43 187.0
21 TraesCS6D01G240100 chr4B 82.753 603 100 4 2 602 429292534 429293134 9.010000e-148 534.0
22 TraesCS6D01G240100 chr4B 85.644 202 23 6 5334 5531 604681536 604681337 2.230000e-49 207.0
23 TraesCS6D01G240100 chr4B 88.430 121 14 0 3404 3524 663766215 663766095 4.930000e-31 147.0
24 TraesCS6D01G240100 chr1A 91.453 351 29 1 1 351 486963937 486964286 1.190000e-131 481.0
25 TraesCS6D01G240100 chr1A 94.231 260 14 1 474 733 487008789 487009047 4.440000e-106 396.0
26 TraesCS6D01G240100 chr1A 100.000 28 0 0 4418 4445 535467524 535467551 1.100000e-02 52.8
27 TraesCS6D01G240100 chr7D 84.146 246 38 1 3 248 375393424 375393180 2.840000e-58 237.0
28 TraesCS6D01G240100 chr3A 77.644 416 55 18 5604 5999 589401117 589400720 1.030000e-52 219.0
29 TraesCS6D01G240100 chr3A 89.831 118 12 0 3408 3525 106611178 106611061 1.060000e-32 152.0
30 TraesCS6D01G240100 chr3B 87.047 193 23 2 5341 5531 349936143 349935951 3.710000e-52 217.0
31 TraesCS6D01G240100 chr3B 87.218 133 14 2 3401 3532 263260724 263260854 1.370000e-31 148.0
32 TraesCS6D01G240100 chr5A 90.083 121 12 0 3404 3524 490696667 490696787 2.280000e-34 158.0
33 TraesCS6D01G240100 chr3D 88.525 122 13 1 3405 3525 555117083 555117204 4.930000e-31 147.0
34 TraesCS6D01G240100 chr4D 88.000 125 12 2 3408 3532 57875246 57875367 1.770000e-30 145.0
35 TraesCS6D01G240100 chr5B 86.260 131 18 0 3403 3533 403545839 403545709 6.380000e-30 143.0
36 TraesCS6D01G240100 chr5B 84.783 138 19 2 3404 3541 517217107 517216972 2.970000e-28 137.0
37 TraesCS6D01G240100 chr5B 84.892 139 17 4 3404 3540 522656737 522656873 2.970000e-28 137.0
38 TraesCS6D01G240100 chr1D 92.308 39 3 0 4414 4452 443718080 443718118 8.550000e-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 TraesCS6D01G240100 chr6D 341193264 341199369 6105 False 11276.0 11276 100.000000 1 6106 1 chr6D.!!$F1 6105
1 TraesCS6D01G240100 chr6A 481255515 481260135 4620 False 2078.0 2828 94.268333 724 5332 3 chr6A.!!$F1 4608
2 TraesCS6D01G240100 chr6B 479078379 479083541 5162 True 1230.2 2763 93.150400 728 6089 5 chr6B.!!$R2 5361
3 TraesCS6D01G240100 chr7A 731880611 731881336 725 True 1164.0 1164 95.592000 1 726 1 chr7A.!!$R1 725
4 TraesCS6D01G240100 chr7A 579091643 579092366 723 False 839.0 839 87.586000 2 726 1 chr7A.!!$F1 724
5 TraesCS6D01G240100 chr5D 332369996 332370661 665 True 1003.0 1003 93.908000 5334 5999 1 chr5D.!!$R1 665
6 TraesCS6D01G240100 chr4A 627604328 627605000 672 True 992.0 992 93.462000 5334 5999 1 chr4A.!!$R2 665
7 TraesCS6D01G240100 chr7B 634169187 634169829 642 False 966.0 966 93.953000 5362 5999 1 chr7B.!!$F1 637
8 TraesCS6D01G240100 chr7B 556496141 556496866 725 True 660.0 660 83.104000 1 726 1 chr7B.!!$R1 725
9 TraesCS6D01G240100 chr1B 662036522 662037207 685 True 909.0 909 91.147000 5335 5999 1 chr1B.!!$R1 664
10 TraesCS6D01G240100 chr2D 14716857 14717584 727 False 806.0 806 86.630000 1 733 1 chr2D.!!$F1 732
11 TraesCS6D01G240100 chr4B 429292534 429293134 600 False 534.0 534 82.753000 2 602 1 chr4B.!!$F1 600

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
815 822 0.613853 TCTTCCTCACCCCGTACAGG 60.614 60.0 0.00 0.0 40.63 4.00 F
1004 1011 0.251341 ACCGGCTGGAAAAAGATGCT 60.251 50.0 21.41 0.0 39.21 3.79 F
2694 2762 0.596600 TGGACAAGCAGACGACGAAC 60.597 55.0 0.00 0.0 0.00 3.95 F
4015 4509 0.464554 GGGGCATTGACTAGCTGTCC 60.465 60.0 11.99 0.0 44.75 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 2546 1.021390 CACGAACCATCTGAGTGGCC 61.021 60.00 0.00 0.0 43.27 5.36 R
2794 2926 4.623002 GGTTCAATTGACCCGCTTAAAAA 58.377 39.13 7.89 0.0 0.00 1.94 R
4236 4734 0.442310 CACGTGGTCCGCAGTATTTG 59.558 55.00 7.95 0.0 41.42 2.32 R
5827 6731 0.109272 TTGGCTAAGCAGACTCGTCG 60.109 55.00 0.00 0.0 34.09 5.12 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
190 191 3.768922 GCACGAGCTCCTCTGGCT 61.769 66.667 8.47 0.00 43.26 4.75
326 327 7.112122 ACATCTCCAACTGCATTGTATCTTTA 58.888 34.615 0.00 0.00 36.47 1.85
438 439 3.254060 GTTCGTGTGACATAGCAGACAT 58.746 45.455 0.00 0.00 32.08 3.06
458 459 6.719370 AGACATCTAGTATCCTCAATCTCCAC 59.281 42.308 0.00 0.00 0.00 4.02
549 550 1.290009 GCTTTGGCACGGCATCTTT 59.710 52.632 6.07 0.00 38.54 2.52
749 750 2.884639 CCCCTTCTTTCACGAACAACAT 59.115 45.455 0.00 0.00 0.00 2.71
753 754 5.440685 CCTTCTTTCACGAACAACATACAC 58.559 41.667 0.00 0.00 0.00 2.90
815 822 0.613853 TCTTCCTCACCCCGTACAGG 60.614 60.000 0.00 0.00 40.63 4.00
1004 1011 0.251341 ACCGGCTGGAAAAAGATGCT 60.251 50.000 21.41 0.00 39.21 3.79
1170 1186 4.596585 CACCACCGCCCCAAACCT 62.597 66.667 0.00 0.00 0.00 3.50
1180 1196 1.024579 CCCCAAACCTCGTCCATTCG 61.025 60.000 0.00 0.00 0.00 3.34
1683 1702 3.382832 ACCAAGCTCGAGGTCGGG 61.383 66.667 24.58 24.97 44.00 5.14
2098 2117 3.241530 TGTGGAGGCGGCTCAAGT 61.242 61.111 36.07 4.01 0.00 3.16
2254 2282 0.957888 GTTCAAGGTGGAGGAGCTGC 60.958 60.000 0.00 0.00 30.84 5.25
2457 2485 6.623767 GCTCACACTGAACTCTTTTCAAGTTT 60.624 38.462 0.00 0.00 37.10 2.66
2458 2486 7.414098 GCTCACACTGAACTCTTTTCAAGTTTA 60.414 37.037 0.00 0.00 37.10 2.01
2460 2488 8.956426 TCACACTGAACTCTTTTCAAGTTTAAT 58.044 29.630 0.00 0.00 37.10 1.40
2481 2546 9.929722 TTTAATAACAAAGAAATCGATGATCGG 57.070 29.630 15.48 0.00 40.88 4.18
2501 2566 1.639298 GCCACTCAGATGGTTCGTGC 61.639 60.000 0.00 0.00 42.28 5.34
2527 2593 8.006298 TCATCCACCACAAATATAAAATCACC 57.994 34.615 0.00 0.00 0.00 4.02
2595 2663 6.775629 AGATTAACTAAACAAAAGAGGGCACA 59.224 34.615 0.00 0.00 0.00 4.57
2596 2664 4.649088 AACTAAACAAAAGAGGGCACAC 57.351 40.909 0.00 0.00 0.00 3.82
2597 2665 3.626930 ACTAAACAAAAGAGGGCACACA 58.373 40.909 0.00 0.00 0.00 3.72
2598 2666 2.959507 AAACAAAAGAGGGCACACAC 57.040 45.000 0.00 0.00 0.00 3.82
2599 2667 2.143876 AACAAAAGAGGGCACACACT 57.856 45.000 0.00 0.00 0.00 3.55
2613 2681 4.994852 GGCACACACTTCTGTTCATTACTA 59.005 41.667 0.00 0.00 0.00 1.82
2614 2682 5.643777 GGCACACACTTCTGTTCATTACTAT 59.356 40.000 0.00 0.00 0.00 2.12
2616 2684 7.201530 GGCACACACTTCTGTTCATTACTATAC 60.202 40.741 0.00 0.00 0.00 1.47
2617 2685 7.545965 GCACACACTTCTGTTCATTACTATACT 59.454 37.037 0.00 0.00 0.00 2.12
2618 2686 9.424319 CACACACTTCTGTTCATTACTATACTT 57.576 33.333 0.00 0.00 0.00 2.24
2690 2758 3.496884 TGTTAATTGGACAAGCAGACGAC 59.503 43.478 0.00 0.00 0.00 4.34
2694 2762 0.596600 TGGACAAGCAGACGACGAAC 60.597 55.000 0.00 0.00 0.00 3.95
2707 2775 1.979469 CGACGAACAAGTAGTGCAGAG 59.021 52.381 0.00 0.00 0.00 3.35
2708 2776 2.604855 CGACGAACAAGTAGTGCAGAGT 60.605 50.000 0.00 0.00 0.00 3.24
2712 2780 5.353938 ACGAACAAGTAGTGCAGAGTTTTA 58.646 37.500 0.00 0.00 0.00 1.52
2742 2868 5.346822 ACATTTCGGAGTACAATGACGTTAC 59.653 40.000 9.21 0.00 33.02 2.50
2743 2869 3.121559 TCGGAGTACAATGACGTTACG 57.878 47.619 2.19 2.19 0.00 3.18
2793 2925 8.508062 TGTGTACAAATACAAACGCATCTTAAT 58.492 29.630 0.00 0.00 42.99 1.40
2794 2926 9.337091 GTGTACAAATACAAACGCATCTTAATT 57.663 29.630 0.00 0.00 42.99 1.40
3019 3152 8.345724 TCGTTATTTCTTTACTAGAGTGGTCT 57.654 34.615 0.00 0.00 33.51 3.85
3132 3287 8.090831 TCTTCTATATGCTTGCTACGATTTCAT 58.909 33.333 0.00 0.00 0.00 2.57
3144 3300 6.543465 TGCTACGATTTCATCCATCTTTTCAT 59.457 34.615 0.00 0.00 0.00 2.57
3149 3305 9.123902 ACGATTTCATCCATCTTTTCATTCATA 57.876 29.630 0.00 0.00 0.00 2.15
3230 3389 3.426859 GCTCTATAGCGGCATATATTGCG 59.573 47.826 1.45 0.00 45.31 4.85
3287 3514 2.320681 ACAAGCTACCTAGTGTCCCA 57.679 50.000 0.00 0.00 0.00 4.37
3296 3523 2.158143 ACCTAGTGTCCCATCTATCCCC 60.158 54.545 0.00 0.00 0.00 4.81
3300 3527 0.832135 TGTCCCATCTATCCCCGCTC 60.832 60.000 0.00 0.00 0.00 5.03
3381 3867 2.484947 GGGGAAATGGGCTCTAGTTACG 60.485 54.545 0.00 0.00 0.00 3.18
3382 3868 2.210961 GGAAATGGGCTCTAGTTACGC 58.789 52.381 0.00 0.00 0.00 4.42
3383 3869 2.419574 GGAAATGGGCTCTAGTTACGCA 60.420 50.000 0.00 0.00 0.00 5.24
3409 3895 8.981724 GAAACCCTTTCTTGGTGAAATATTAC 57.018 34.615 0.00 0.00 42.96 1.89
3410 3896 8.721133 AAACCCTTTCTTGGTGAAATATTACT 57.279 30.769 0.00 0.00 42.96 2.24
3411 3897 7.939784 ACCCTTTCTTGGTGAAATATTACTC 57.060 36.000 0.00 0.00 42.96 2.59
3412 3898 6.890268 ACCCTTTCTTGGTGAAATATTACTCC 59.110 38.462 0.00 0.00 42.96 3.85
3413 3899 6.321435 CCCTTTCTTGGTGAAATATTACTCCC 59.679 42.308 0.00 0.00 42.96 4.30
3414 3900 7.119387 CCTTTCTTGGTGAAATATTACTCCCT 58.881 38.462 0.00 0.00 42.96 4.20
3415 3901 7.615757 CCTTTCTTGGTGAAATATTACTCCCTT 59.384 37.037 0.00 0.00 42.96 3.95
3416 3902 8.950007 TTTCTTGGTGAAATATTACTCCCTTT 57.050 30.769 0.00 0.00 39.50 3.11
3417 3903 7.938140 TCTTGGTGAAATATTACTCCCTTTG 57.062 36.000 0.00 0.00 0.00 2.77
3418 3904 7.466804 TCTTGGTGAAATATTACTCCCTTTGT 58.533 34.615 0.00 0.00 0.00 2.83
3419 3905 7.610305 TCTTGGTGAAATATTACTCCCTTTGTC 59.390 37.037 0.00 0.00 0.00 3.18
3420 3906 7.027874 TGGTGAAATATTACTCCCTTTGTCT 57.972 36.000 0.00 0.00 0.00 3.41
3421 3907 6.884295 TGGTGAAATATTACTCCCTTTGTCTG 59.116 38.462 0.00 0.00 0.00 3.51
3422 3908 6.318900 GGTGAAATATTACTCCCTTTGTCTGG 59.681 42.308 0.00 0.00 0.00 3.86
3423 3909 6.318900 GTGAAATATTACTCCCTTTGTCTGGG 59.681 42.308 0.00 0.00 45.90 4.45
3434 3920 3.684788 CCTTTGTCTGGGAATACTTGTCG 59.315 47.826 0.00 0.00 0.00 4.35
3435 3921 3.328382 TTGTCTGGGAATACTTGTCGG 57.672 47.619 0.00 0.00 0.00 4.79
3436 3922 2.531771 TGTCTGGGAATACTTGTCGGA 58.468 47.619 0.00 0.00 0.00 4.55
3437 3923 3.104512 TGTCTGGGAATACTTGTCGGAT 58.895 45.455 0.00 0.00 0.00 4.18
3438 3924 4.283337 TGTCTGGGAATACTTGTCGGATA 58.717 43.478 0.00 0.00 0.00 2.59
3439 3925 4.712829 TGTCTGGGAATACTTGTCGGATAA 59.287 41.667 0.00 0.00 0.00 1.75
3440 3926 5.188163 TGTCTGGGAATACTTGTCGGATAAA 59.812 40.000 0.00 0.00 0.00 1.40
3441 3927 6.126883 TGTCTGGGAATACTTGTCGGATAAAT 60.127 38.462 0.00 0.00 0.00 1.40
3442 3928 6.202954 GTCTGGGAATACTTGTCGGATAAATG 59.797 42.308 0.00 0.00 0.00 2.32
3443 3929 6.099125 TCTGGGAATACTTGTCGGATAAATGA 59.901 38.462 0.00 0.00 0.00 2.57
3444 3930 6.654959 TGGGAATACTTGTCGGATAAATGAA 58.345 36.000 0.00 0.00 0.00 2.57
3445 3931 7.287061 TGGGAATACTTGTCGGATAAATGAAT 58.713 34.615 0.00 0.00 0.00 2.57
3446 3932 8.433599 TGGGAATACTTGTCGGATAAATGAATA 58.566 33.333 0.00 0.00 0.00 1.75
3447 3933 9.280174 GGGAATACTTGTCGGATAAATGAATAA 57.720 33.333 0.00 0.00 0.00 1.40
3452 3938 8.889849 ACTTGTCGGATAAATGAATAAAAACG 57.110 30.769 0.00 0.00 0.00 3.60
3453 3939 7.966204 ACTTGTCGGATAAATGAATAAAAACGG 59.034 33.333 0.00 0.00 0.00 4.44
3454 3940 7.612668 TGTCGGATAAATGAATAAAAACGGA 57.387 32.000 0.00 0.00 0.00 4.69
3455 3941 8.215926 TGTCGGATAAATGAATAAAAACGGAT 57.784 30.769 0.00 0.00 0.00 4.18
3456 3942 9.327628 TGTCGGATAAATGAATAAAAACGGATA 57.672 29.630 0.00 0.00 0.00 2.59
3495 3981 9.965902 AAATACATCTAGATACATCCATTTCCC 57.034 33.333 4.54 0.00 0.00 3.97
3496 3982 6.380079 ACATCTAGATACATCCATTTCCCC 57.620 41.667 4.54 0.00 0.00 4.81
3497 3983 5.046304 ACATCTAGATACATCCATTTCCCCG 60.046 44.000 4.54 0.00 0.00 5.73
3498 3984 4.747583 TCTAGATACATCCATTTCCCCGA 58.252 43.478 0.00 0.00 0.00 5.14
3499 3985 3.771577 AGATACATCCATTTCCCCGAC 57.228 47.619 0.00 0.00 0.00 4.79
3500 3986 3.045634 AGATACATCCATTTCCCCGACA 58.954 45.455 0.00 0.00 0.00 4.35
3501 3987 3.458118 AGATACATCCATTTCCCCGACAA 59.542 43.478 0.00 0.00 0.00 3.18
3502 3988 2.128771 ACATCCATTTCCCCGACAAG 57.871 50.000 0.00 0.00 0.00 3.16
3503 3989 1.354368 ACATCCATTTCCCCGACAAGT 59.646 47.619 0.00 0.00 0.00 3.16
3504 3990 2.574369 ACATCCATTTCCCCGACAAGTA 59.426 45.455 0.00 0.00 0.00 2.24
3505 3991 3.202151 ACATCCATTTCCCCGACAAGTAT 59.798 43.478 0.00 0.00 0.00 2.12
3506 3992 4.207165 CATCCATTTCCCCGACAAGTATT 58.793 43.478 0.00 0.00 0.00 1.89
3507 3993 4.310022 TCCATTTCCCCGACAAGTATTT 57.690 40.909 0.00 0.00 0.00 1.40
3508 3994 4.266714 TCCATTTCCCCGACAAGTATTTC 58.733 43.478 0.00 0.00 0.00 2.17
3509 3995 4.018779 TCCATTTCCCCGACAAGTATTTCT 60.019 41.667 0.00 0.00 0.00 2.52
3510 3996 4.096382 CCATTTCCCCGACAAGTATTTCTG 59.904 45.833 0.00 0.00 0.00 3.02
3511 3997 3.343941 TTCCCCGACAAGTATTTCTGG 57.656 47.619 0.00 0.00 0.00 3.86
3512 3998 2.542550 TCCCCGACAAGTATTTCTGGA 58.457 47.619 0.00 0.00 0.00 3.86
3513 3999 2.235402 TCCCCGACAAGTATTTCTGGAC 59.765 50.000 0.00 0.00 0.00 4.02
3514 4000 2.268298 CCCGACAAGTATTTCTGGACG 58.732 52.381 0.00 0.00 35.64 4.79
3515 4001 2.094390 CCCGACAAGTATTTCTGGACGA 60.094 50.000 0.00 0.00 37.43 4.20
3516 4002 3.581755 CCGACAAGTATTTCTGGACGAA 58.418 45.455 0.00 0.00 37.43 3.85
3517 4003 3.991773 CCGACAAGTATTTCTGGACGAAA 59.008 43.478 0.00 0.00 45.08 3.46
3518 4004 4.091509 CCGACAAGTATTTCTGGACGAAAG 59.908 45.833 0.00 0.00 44.29 2.62
3519 4005 4.091509 CGACAAGTATTTCTGGACGAAAGG 59.908 45.833 0.00 0.00 44.29 3.11
3520 4006 5.223449 ACAAGTATTTCTGGACGAAAGGA 57.777 39.130 0.00 0.00 44.29 3.36
3521 4007 5.238583 ACAAGTATTTCTGGACGAAAGGAG 58.761 41.667 0.00 0.00 44.29 3.69
3551 4037 8.768955 GTGATATCAAACTTCACATGATACCTC 58.231 37.037 7.07 0.00 38.48 3.85
3559 4045 5.899547 ACTTCACATGATACCTCTGATACCA 59.100 40.000 0.00 0.00 0.00 3.25
3755 4241 1.661341 GAGACATGGCATCACTGGAC 58.339 55.000 0.00 0.00 0.00 4.02
3786 4272 1.601419 TTTCTACCCTCACCGCCTCG 61.601 60.000 0.00 0.00 0.00 4.63
3868 4354 3.552541 CTCGAATATGAACCCGAGTACG 58.447 50.000 0.00 0.00 42.29 3.67
3913 4399 2.871182 TGCTACCATCAGCTTACTCG 57.129 50.000 0.00 0.00 42.30 4.18
3916 4402 2.546795 GCTACCATCAGCTTACTCGCAT 60.547 50.000 0.00 0.00 38.57 4.73
4015 4509 0.464554 GGGGCATTGACTAGCTGTCC 60.465 60.000 11.99 0.00 44.75 4.02
4099 4593 6.095377 CCAAGAAAAGGATATGACAAGCAAC 58.905 40.000 0.00 0.00 0.00 4.17
4206 4701 2.042686 TCTGCTCATTGCCATGTACC 57.957 50.000 0.00 0.00 42.00 3.34
4212 4710 3.682718 GCTCATTGCCATGTACCAGTACT 60.683 47.826 9.24 0.00 34.89 2.73
4216 4714 4.465632 TTGCCATGTACCAGTACTAGTG 57.534 45.455 5.39 5.79 37.00 2.74
4236 4734 6.727824 AGTGAGAGTGCAACAAATATACAC 57.272 37.500 0.00 0.00 41.43 2.90
4244 4743 9.277565 GAGTGCAACAAATATACACAAATACTG 57.722 33.333 0.00 0.00 41.43 2.74
4247 4746 6.196353 GCAACAAATATACACAAATACTGCGG 59.804 38.462 0.00 0.00 0.00 5.69
4250 4749 6.037830 ACAAATATACACAAATACTGCGGACC 59.962 38.462 0.00 0.00 0.00 4.46
4282 4832 8.594687 GTTAAAACGGATCGTAAATACTAGCAA 58.405 33.333 0.00 0.00 39.99 3.91
4283 4833 7.781548 AAAACGGATCGTAAATACTAGCAAT 57.218 32.000 0.00 0.00 39.99 3.56
4291 4841 7.385778 TCGTAAATACTAGCAATTGCCTTTT 57.614 32.000 26.45 18.87 43.38 2.27
4297 4847 9.942850 AAATACTAGCAATTGCCTTTTAAATGT 57.057 25.926 26.45 13.42 43.38 2.71
4300 4850 8.122472 ACTAGCAATTGCCTTTTAAATGTACT 57.878 30.769 26.45 5.58 43.38 2.73
4302 4852 6.758254 AGCAATTGCCTTTTAAATGTACTGT 58.242 32.000 26.45 0.00 43.38 3.55
4305 4855 7.596995 GCAATTGCCTTTTAAATGTACTGTACA 59.403 33.333 21.68 21.68 37.89 2.90
4306 4856 9.469807 CAATTGCCTTTTAAATGTACTGTACAA 57.530 29.630 23.03 5.78 42.76 2.41
4307 4857 9.691362 AATTGCCTTTTAAATGTACTGTACAAG 57.309 29.630 23.03 14.56 42.76 3.16
4321 4871 9.850628 TGTACTGTACAAGTTTATAAGTAGCTG 57.149 33.333 17.74 0.00 40.56 4.24
4748 5298 0.034756 TCACCACCAAGATGGACGTG 59.965 55.000 2.85 8.49 43.02 4.49
5145 5698 5.551233 ACTGCTCTGCTTTGTAGTTAATCA 58.449 37.500 0.00 0.00 0.00 2.57
5148 5701 5.409520 TGCTCTGCTTTGTAGTTAATCAGTG 59.590 40.000 0.00 0.00 0.00 3.66
5183 5736 1.561542 AGCTAGCTGGTGGTAAGCATT 59.438 47.619 18.57 0.00 43.37 3.56
5255 5808 2.224066 CCGTGAGATTATCCTGTGGGTC 60.224 54.545 0.00 0.00 0.00 4.46
5263 5816 6.441222 AGATTATCCTGTGGGTCAAGTAGTA 58.559 40.000 0.00 0.00 0.00 1.82
5264 5817 7.076446 AGATTATCCTGTGGGTCAAGTAGTAT 58.924 38.462 0.00 0.00 0.00 2.12
5265 5818 8.232412 AGATTATCCTGTGGGTCAAGTAGTATA 58.768 37.037 0.00 0.00 0.00 1.47
5305 6187 4.569564 GTGAGTGGAAAATACACGGGATAC 59.430 45.833 0.00 0.00 43.41 2.24
5338 6221 6.408035 TCAGTATATTTTTACGTTCAGGCCA 58.592 36.000 5.01 0.00 0.00 5.36
5360 6243 6.426633 GCCATGTTTGGTAGCAAAGTATTTTT 59.573 34.615 19.87 0.00 45.57 1.94
5474 6360 6.345096 ACTTTAGTATTGGCAAAACTGCAT 57.655 33.333 3.01 0.00 36.33 3.96
5542 6429 3.257393 CTGAGCAGCTAACAAGAACGAT 58.743 45.455 0.00 0.00 0.00 3.73
5550 6437 5.734498 CAGCTAACAAGAACGATATTGCAAC 59.266 40.000 0.00 0.00 30.83 4.17
5554 6441 6.656314 AACAAGAACGATATTGCAACGATA 57.344 33.333 14.04 0.00 30.83 2.92
5561 6448 3.245048 CGATATTGCAACGATACAGTGCA 59.755 43.478 0.00 0.00 0.00 4.57
5579 6466 2.079158 GCACTGCATTGAGCTTGACTA 58.921 47.619 8.44 0.00 45.94 2.59
5827 6731 1.456296 CTAGCCCCGTTGGTAAAACC 58.544 55.000 0.00 0.00 39.22 3.27
6043 6952 9.988815 ATACTTTACTATCAAACATAGCCTCAG 57.011 33.333 0.00 0.00 0.00 3.35
6072 6981 6.721571 TTTTATAACAGGACGAGAAGCTTG 57.278 37.500 2.10 0.00 0.00 4.01
6078 6987 0.603569 GGACGAGAAGCTTGTCTCCA 59.396 55.000 24.50 0.00 42.71 3.86
6085 6994 0.034670 AAGCTTGTCTCCATGCCCTC 60.035 55.000 0.00 0.00 41.41 4.30
6089 6998 0.982852 TTGTCTCCATGCCCTCCGAT 60.983 55.000 0.00 0.00 0.00 4.18
6090 6999 0.105709 TGTCTCCATGCCCTCCGATA 60.106 55.000 0.00 0.00 0.00 2.92
6091 7000 0.605589 GTCTCCATGCCCTCCGATAG 59.394 60.000 0.00 0.00 0.00 2.08
6092 7001 0.188587 TCTCCATGCCCTCCGATAGT 59.811 55.000 0.00 0.00 0.00 2.12
6093 7002 1.427753 TCTCCATGCCCTCCGATAGTA 59.572 52.381 0.00 0.00 0.00 1.82
6094 7003 2.158370 TCTCCATGCCCTCCGATAGTAA 60.158 50.000 0.00 0.00 0.00 2.24
6095 7004 2.834549 CTCCATGCCCTCCGATAGTAAT 59.165 50.000 0.00 0.00 0.00 1.89
6096 7005 2.567169 TCCATGCCCTCCGATAGTAATG 59.433 50.000 0.00 0.00 0.00 1.90
6097 7006 2.355108 CCATGCCCTCCGATAGTAATGG 60.355 54.545 0.00 0.00 0.00 3.16
6098 7007 2.391926 TGCCCTCCGATAGTAATGGA 57.608 50.000 0.00 0.00 0.00 3.41
6099 7008 2.684943 TGCCCTCCGATAGTAATGGAA 58.315 47.619 0.00 0.00 0.00 3.53
6100 7009 3.042682 TGCCCTCCGATAGTAATGGAAA 58.957 45.455 0.00 0.00 0.00 3.13
6101 7010 3.181458 TGCCCTCCGATAGTAATGGAAAC 60.181 47.826 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 191 5.432680 AGGAAGAATGAGAAGAGAATGCA 57.567 39.130 0.00 0.00 0.00 3.96
549 550 1.274167 ACGTTCTGGAGCCGTATTTGA 59.726 47.619 0.00 0.00 32.22 2.69
582 583 3.127533 GTGCATGGGTCGCTGGAC 61.128 66.667 0.00 0.00 42.66 4.02
749 750 1.154357 CTACGTGTCGCGCTGTGTA 60.154 57.895 5.56 0.83 46.11 2.90
753 754 3.827784 GCACTACGTGTCGCGCTG 61.828 66.667 5.56 0.00 46.11 5.18
841 848 0.716108 CGCTTCGACTAGCAACAAGG 59.284 55.000 9.63 0.00 41.28 3.61
921 928 2.497092 CGCGTTCTCGTGTGGATCG 61.497 63.158 0.00 0.00 41.80 3.69
1087 1100 1.505353 GATGGTGTTGAGCTGCTGC 59.495 57.895 7.01 7.62 40.05 5.25
1088 1101 0.952497 ACGATGGTGTTGAGCTGCTG 60.952 55.000 7.01 0.00 0.00 4.41
1160 1176 1.304134 AATGGACGAGGTTTGGGGC 60.304 57.895 0.00 0.00 0.00 5.80
1170 1186 3.833645 CGGAGGGCGAATGGACGA 61.834 66.667 0.00 0.00 35.09 4.20
1234 1253 4.694233 CAGGCAGAGCAGCGTGGT 62.694 66.667 9.67 0.00 44.28 4.16
1683 1702 1.376812 GGGGAACGTGACCATGTCC 60.377 63.158 12.88 3.31 0.00 4.02
1758 1777 3.807538 GTGTCGCCCTGCTGCATG 61.808 66.667 1.31 0.00 0.00 4.06
1857 1876 2.224549 CGGCACTAGTATCTCGGAGAAG 59.775 54.545 12.40 7.32 34.09 2.85
2070 2089 4.421515 CTCCACAGGCAGCCCAGG 62.422 72.222 8.22 8.03 0.00 4.45
2337 2365 4.582869 CATCCCACTTCATCTTCTTCACA 58.417 43.478 0.00 0.00 0.00 3.58
2457 2485 7.307751 GCCCGATCATCGATTTCTTTGTTATTA 60.308 37.037 9.16 0.00 43.74 0.98
2458 2486 6.513393 GCCCGATCATCGATTTCTTTGTTATT 60.513 38.462 9.16 0.00 43.74 1.40
2460 2488 4.272504 GCCCGATCATCGATTTCTTTGTTA 59.727 41.667 9.16 0.00 43.74 2.41
2480 2545 1.450312 CGAACCATCTGAGTGGCCC 60.450 63.158 0.00 0.00 43.27 5.80
2481 2546 1.021390 CACGAACCATCTGAGTGGCC 61.021 60.000 0.00 0.00 43.27 5.36
2501 2566 8.137437 GGTGATTTTATATTTGTGGTGGATGAG 58.863 37.037 0.00 0.00 0.00 2.90
2527 2593 5.744666 ATAAAATTGTTATGTCCCCGTCG 57.255 39.130 0.00 0.00 0.00 5.12
2568 2636 8.235226 GTGCCCTCTTTTGTTTAGTTAATCTAC 58.765 37.037 0.00 0.00 0.00 2.59
2569 2637 7.940137 TGTGCCCTCTTTTGTTTAGTTAATCTA 59.060 33.333 0.00 0.00 0.00 1.98
2570 2638 6.775629 TGTGCCCTCTTTTGTTTAGTTAATCT 59.224 34.615 0.00 0.00 0.00 2.40
2652 2720 9.753674 TCCAATTAACAAACTTCTCCTATCAAT 57.246 29.630 0.00 0.00 0.00 2.57
2653 2721 9.010029 GTCCAATTAACAAACTTCTCCTATCAA 57.990 33.333 0.00 0.00 0.00 2.57
2654 2722 8.160765 TGTCCAATTAACAAACTTCTCCTATCA 58.839 33.333 0.00 0.00 0.00 2.15
2655 2723 8.561738 TGTCCAATTAACAAACTTCTCCTATC 57.438 34.615 0.00 0.00 0.00 2.08
2656 2724 8.934023 TTGTCCAATTAACAAACTTCTCCTAT 57.066 30.769 3.71 0.00 33.86 2.57
2657 2725 7.040686 GCTTGTCCAATTAACAAACTTCTCCTA 60.041 37.037 6.93 0.00 36.27 2.94
2658 2726 6.239036 GCTTGTCCAATTAACAAACTTCTCCT 60.239 38.462 6.93 0.00 36.27 3.69
2659 2727 5.920840 GCTTGTCCAATTAACAAACTTCTCC 59.079 40.000 6.93 0.00 36.27 3.71
2660 2728 6.503524 TGCTTGTCCAATTAACAAACTTCTC 58.496 36.000 6.93 0.00 36.27 2.87
2661 2729 6.321181 TCTGCTTGTCCAATTAACAAACTTCT 59.679 34.615 6.93 0.00 36.27 2.85
2662 2730 6.417930 GTCTGCTTGTCCAATTAACAAACTTC 59.582 38.462 6.93 0.23 36.27 3.01
2690 2758 4.795970 AAAACTCTGCACTACTTGTTCG 57.204 40.909 0.00 0.00 0.00 3.95
2694 2762 9.419297 TGTAAGTATAAAACTCTGCACTACTTG 57.581 33.333 0.00 0.00 37.50 3.16
2712 2780 7.434307 CGTCATTGTACTCCGAAATGTAAGTAT 59.566 37.037 0.00 0.00 33.84 2.12
2742 2868 5.390613 ACAAAAAGAAGACAGTTTGTGACG 58.609 37.500 0.16 0.00 41.40 4.35
2743 2869 7.501515 CAAACAAAAAGAAGACAGTTTGTGAC 58.498 34.615 0.00 0.00 41.94 3.67
2794 2926 4.623002 GGTTCAATTGACCCGCTTAAAAA 58.377 39.130 7.89 0.00 0.00 1.94
3008 3141 9.307121 CAACAACTGATAAATAGACCACTCTAG 57.693 37.037 0.00 0.00 32.24 2.43
3014 3147 6.371548 GCAGACAACAACTGATAAATAGACCA 59.628 38.462 0.00 0.00 37.54 4.02
3019 3152 7.620880 AGTAGGCAGACAACAACTGATAAATA 58.379 34.615 0.00 0.00 37.54 1.40
3132 3287 7.824289 ACTTTCGTCTATGAATGAAAAGATGGA 59.176 33.333 0.00 0.00 30.67 3.41
3144 3300 5.163540 GGCTCCTTCTACTTTCGTCTATGAA 60.164 44.000 0.00 0.00 0.00 2.57
3149 3305 2.526432 TGGCTCCTTCTACTTTCGTCT 58.474 47.619 0.00 0.00 0.00 4.18
3158 3317 1.200760 TGGCTGCTTGGCTCCTTCTA 61.201 55.000 0.00 0.00 42.34 2.10
3193 3352 5.874261 GCTATAGAGCTTCATCCCAATTCTC 59.126 44.000 3.21 0.00 45.98 2.87
3225 3384 3.570822 TTTGCCCCGGTACCGCAAT 62.571 57.895 29.15 0.00 41.78 3.56
3226 3385 4.266543 TTTGCCCCGGTACCGCAA 62.267 61.111 29.15 23.05 40.58 4.85
3230 3389 0.038021 TTTAGGTTTGCCCCGGTACC 59.962 55.000 0.16 0.16 34.57 3.34
3342 3569 2.035449 CCCCCTTTGTTTTCTCGAAACC 59.965 50.000 0.00 0.00 45.66 3.27
3412 3898 3.684788 CGACAAGTATTCCCAGACAAAGG 59.315 47.826 0.00 0.00 0.00 3.11
3413 3899 3.684788 CCGACAAGTATTCCCAGACAAAG 59.315 47.826 0.00 0.00 0.00 2.77
3414 3900 3.325425 TCCGACAAGTATTCCCAGACAAA 59.675 43.478 0.00 0.00 0.00 2.83
3415 3901 2.901192 TCCGACAAGTATTCCCAGACAA 59.099 45.455 0.00 0.00 0.00 3.18
3416 3902 2.531771 TCCGACAAGTATTCCCAGACA 58.468 47.619 0.00 0.00 0.00 3.41
3417 3903 3.821421 ATCCGACAAGTATTCCCAGAC 57.179 47.619 0.00 0.00 0.00 3.51
3418 3904 5.943349 TTTATCCGACAAGTATTCCCAGA 57.057 39.130 0.00 0.00 0.00 3.86
3419 3905 6.288294 TCATTTATCCGACAAGTATTCCCAG 58.712 40.000 0.00 0.00 0.00 4.45
3420 3906 6.241882 TCATTTATCCGACAAGTATTCCCA 57.758 37.500 0.00 0.00 0.00 4.37
3421 3907 7.745620 ATTCATTTATCCGACAAGTATTCCC 57.254 36.000 0.00 0.00 0.00 3.97
3426 3912 9.976255 CGTTTTTATTCATTTATCCGACAAGTA 57.024 29.630 0.00 0.00 0.00 2.24
3427 3913 7.966204 CCGTTTTTATTCATTTATCCGACAAGT 59.034 33.333 0.00 0.00 0.00 3.16
3428 3914 8.178964 TCCGTTTTTATTCATTTATCCGACAAG 58.821 33.333 0.00 0.00 0.00 3.16
3429 3915 8.041829 TCCGTTTTTATTCATTTATCCGACAA 57.958 30.769 0.00 0.00 0.00 3.18
3430 3916 7.612668 TCCGTTTTTATTCATTTATCCGACA 57.387 32.000 0.00 0.00 0.00 4.35
3469 3955 9.965902 GGGAAATGGATGTATCTAGATGTATTT 57.034 33.333 15.79 11.36 0.00 1.40
3470 3956 8.552296 GGGGAAATGGATGTATCTAGATGTATT 58.448 37.037 15.79 4.32 0.00 1.89
3471 3957 7.147655 CGGGGAAATGGATGTATCTAGATGTAT 60.148 40.741 15.79 9.11 0.00 2.29
3472 3958 6.154534 CGGGGAAATGGATGTATCTAGATGTA 59.845 42.308 15.79 4.44 0.00 2.29
3473 3959 5.046304 CGGGGAAATGGATGTATCTAGATGT 60.046 44.000 15.79 1.25 0.00 3.06
3474 3960 5.187772 TCGGGGAAATGGATGTATCTAGATG 59.812 44.000 15.79 0.00 0.00 2.90
3475 3961 5.187967 GTCGGGGAAATGGATGTATCTAGAT 59.812 44.000 10.73 10.73 0.00 1.98
3476 3962 4.527038 GTCGGGGAAATGGATGTATCTAGA 59.473 45.833 0.00 0.00 0.00 2.43
3477 3963 4.283467 TGTCGGGGAAATGGATGTATCTAG 59.717 45.833 0.00 0.00 0.00 2.43
3478 3964 4.228010 TGTCGGGGAAATGGATGTATCTA 58.772 43.478 0.00 0.00 0.00 1.98
3479 3965 3.045634 TGTCGGGGAAATGGATGTATCT 58.954 45.455 0.00 0.00 0.00 1.98
3480 3966 3.485463 TGTCGGGGAAATGGATGTATC 57.515 47.619 0.00 0.00 0.00 2.24
3481 3967 3.202151 ACTTGTCGGGGAAATGGATGTAT 59.798 43.478 0.00 0.00 0.00 2.29
3482 3968 2.574369 ACTTGTCGGGGAAATGGATGTA 59.426 45.455 0.00 0.00 0.00 2.29
3483 3969 1.354368 ACTTGTCGGGGAAATGGATGT 59.646 47.619 0.00 0.00 0.00 3.06
3484 3970 2.128771 ACTTGTCGGGGAAATGGATG 57.871 50.000 0.00 0.00 0.00 3.51
3485 3971 4.519906 AATACTTGTCGGGGAAATGGAT 57.480 40.909 0.00 0.00 0.00 3.41
3486 3972 4.018779 AGAAATACTTGTCGGGGAAATGGA 60.019 41.667 0.00 0.00 0.00 3.41
3487 3973 4.096382 CAGAAATACTTGTCGGGGAAATGG 59.904 45.833 0.00 0.00 0.00 3.16
3488 3974 4.096382 CCAGAAATACTTGTCGGGGAAATG 59.904 45.833 0.00 0.00 0.00 2.32
3489 3975 4.018779 TCCAGAAATACTTGTCGGGGAAAT 60.019 41.667 0.00 0.00 30.83 2.17
3490 3976 3.328343 TCCAGAAATACTTGTCGGGGAAA 59.672 43.478 0.00 0.00 30.83 3.13
3491 3977 2.907696 TCCAGAAATACTTGTCGGGGAA 59.092 45.455 0.00 0.00 30.83 3.97
3492 3978 2.235402 GTCCAGAAATACTTGTCGGGGA 59.765 50.000 0.00 0.00 30.83 4.81
3493 3979 2.629051 GTCCAGAAATACTTGTCGGGG 58.371 52.381 0.00 0.00 30.83 5.73
3494 3980 2.094390 TCGTCCAGAAATACTTGTCGGG 60.094 50.000 0.00 0.00 0.00 5.14
3495 3981 3.226346 TCGTCCAGAAATACTTGTCGG 57.774 47.619 0.00 0.00 0.00 4.79
3496 3982 4.091509 CCTTTCGTCCAGAAATACTTGTCG 59.908 45.833 0.00 0.00 46.60 4.35
3497 3983 5.235516 TCCTTTCGTCCAGAAATACTTGTC 58.764 41.667 0.00 0.00 46.60 3.18
3498 3984 5.221661 ACTCCTTTCGTCCAGAAATACTTGT 60.222 40.000 0.00 0.00 46.60 3.16
3499 3985 5.238583 ACTCCTTTCGTCCAGAAATACTTG 58.761 41.667 0.00 0.00 46.60 3.16
3500 3986 5.485209 ACTCCTTTCGTCCAGAAATACTT 57.515 39.130 0.00 0.00 46.60 2.24
3501 3987 5.127356 CCTACTCCTTTCGTCCAGAAATACT 59.873 44.000 0.00 0.00 46.60 2.12
3502 3988 5.105432 ACCTACTCCTTTCGTCCAGAAATAC 60.105 44.000 0.00 0.00 46.60 1.89
3503 3989 5.021458 ACCTACTCCTTTCGTCCAGAAATA 58.979 41.667 0.00 0.00 46.60 1.40
3504 3990 3.838903 ACCTACTCCTTTCGTCCAGAAAT 59.161 43.478 0.00 0.00 46.60 2.17
3505 3991 3.006537 CACCTACTCCTTTCGTCCAGAAA 59.993 47.826 0.00 0.00 45.76 2.52
3506 3992 2.561419 CACCTACTCCTTTCGTCCAGAA 59.439 50.000 0.00 0.00 37.01 3.02
3507 3993 2.168496 CACCTACTCCTTTCGTCCAGA 58.832 52.381 0.00 0.00 0.00 3.86
3508 3994 2.168496 TCACCTACTCCTTTCGTCCAG 58.832 52.381 0.00 0.00 0.00 3.86
3509 3995 2.297698 TCACCTACTCCTTTCGTCCA 57.702 50.000 0.00 0.00 0.00 4.02
3510 3996 4.583489 TGATATCACCTACTCCTTTCGTCC 59.417 45.833 0.00 0.00 0.00 4.79
3511 3997 5.769484 TGATATCACCTACTCCTTTCGTC 57.231 43.478 0.00 0.00 0.00 4.20
3512 3998 6.154706 AGTTTGATATCACCTACTCCTTTCGT 59.845 38.462 4.48 0.00 0.00 3.85
3513 3999 6.574350 AGTTTGATATCACCTACTCCTTTCG 58.426 40.000 4.48 0.00 0.00 3.46
3514 4000 8.041323 TGAAGTTTGATATCACCTACTCCTTTC 58.959 37.037 4.48 5.01 0.00 2.62
3515 4001 7.824779 GTGAAGTTTGATATCACCTACTCCTTT 59.175 37.037 4.48 0.00 37.97 3.11
3516 4002 7.038302 TGTGAAGTTTGATATCACCTACTCCTT 60.038 37.037 4.48 0.36 42.12 3.36
3517 4003 6.440647 TGTGAAGTTTGATATCACCTACTCCT 59.559 38.462 4.48 0.00 42.12 3.69
3518 4004 6.640518 TGTGAAGTTTGATATCACCTACTCC 58.359 40.000 4.48 0.00 42.12 3.85
3519 4005 7.981789 TCATGTGAAGTTTGATATCACCTACTC 59.018 37.037 4.48 1.36 42.12 2.59
3520 4006 7.851228 TCATGTGAAGTTTGATATCACCTACT 58.149 34.615 4.48 6.70 42.12 2.57
3521 4007 8.668510 ATCATGTGAAGTTTGATATCACCTAC 57.331 34.615 4.48 4.44 42.12 3.18
3551 4037 7.621428 ATTGAAGTTTGAGATGTGGTATCAG 57.379 36.000 0.00 0.00 28.26 2.90
3679 4165 3.656559 AGCATGTGTGAAATTGGCTTTC 58.343 40.909 0.00 0.00 43.05 2.62
3725 4211 4.159377 TGCCATGTCTCGAAATTCAAAC 57.841 40.909 0.00 0.00 0.00 2.93
3755 4241 3.379452 AGGGTAGAAAGAGTGGGAGATG 58.621 50.000 0.00 0.00 0.00 2.90
3786 4272 0.447801 AATCGTTGAATGCGCAGACC 59.552 50.000 18.32 7.92 0.00 3.85
3892 4378 3.119291 CGAGTAAGCTGATGGTAGCAAG 58.881 50.000 0.00 0.00 46.07 4.01
3916 4402 1.444383 GTGATCAGCGTGCGACTCA 60.444 57.895 0.00 0.00 0.00 3.41
3946 4439 5.415389 AGCAGCCTTTGTTGAAAAATGTTTT 59.585 32.000 0.00 0.00 0.00 2.43
3981 4475 1.141019 CCCCCATCGTACGTGTCAG 59.859 63.158 16.05 2.93 0.00 3.51
4174 4669 1.209261 TGAGCAGATTCGGCATTGGTA 59.791 47.619 11.37 0.00 0.00 3.25
4206 4701 4.505313 TGTTGCACTCTCACTAGTACTG 57.495 45.455 5.39 0.00 0.00 2.74
4212 4710 7.382898 TGTGTATATTTGTTGCACTCTCACTA 58.617 34.615 0.00 0.00 0.00 2.74
4216 4714 9.490663 GTATTTGTGTATATTTGTTGCACTCTC 57.509 33.333 0.00 0.00 0.00 3.20
4236 4734 0.442310 CACGTGGTCCGCAGTATTTG 59.558 55.000 7.95 0.00 41.42 2.32
4250 4749 1.794116 ACGATCCGTTTTAACCACGTG 59.206 47.619 9.08 9.08 36.35 4.49
4253 4803 7.294676 AGTATTTACGATCCGTTTTAACCAC 57.705 36.000 0.00 0.00 41.54 4.16
4282 4832 8.856103 ACTTGTACAGTACATTTAAAAGGCAAT 58.144 29.630 14.34 0.00 38.68 3.56
4283 4833 8.228035 ACTTGTACAGTACATTTAAAAGGCAA 57.772 30.769 14.34 0.00 38.68 4.52
4295 4845 9.850628 CAGCTACTTATAAACTTGTACAGTACA 57.149 33.333 9.51 9.51 32.94 2.90
4296 4846 9.298774 CCAGCTACTTATAAACTTGTACAGTAC 57.701 37.037 3.49 3.49 32.94 2.73
4297 4847 9.246670 TCCAGCTACTTATAAACTTGTACAGTA 57.753 33.333 0.00 0.00 32.94 2.74
4298 4848 8.033626 GTCCAGCTACTTATAAACTTGTACAGT 58.966 37.037 0.00 0.00 37.30 3.55
4300 4850 7.898918 TGTCCAGCTACTTATAAACTTGTACA 58.101 34.615 0.00 0.00 0.00 2.90
4302 4852 8.755028 TCATGTCCAGCTACTTATAAACTTGTA 58.245 33.333 0.00 0.00 0.00 2.41
5145 5698 1.267261 GCTATATCGTCCGTGCTCACT 59.733 52.381 0.00 0.00 0.00 3.41
5148 5701 2.476519 GCTAGCTATATCGTCCGTGCTC 60.477 54.545 7.70 0.00 32.72 4.26
5263 5816 7.554118 CCACTCACTCATGATTTTTGGTACTAT 59.446 37.037 0.00 0.00 33.22 2.12
5264 5817 6.878923 CCACTCACTCATGATTTTTGGTACTA 59.121 38.462 0.00 0.00 33.22 1.82
5265 5818 5.707298 CCACTCACTCATGATTTTTGGTACT 59.293 40.000 0.00 0.00 33.22 2.73
5280 6162 3.000727 CCCGTGTATTTTCCACTCACTC 58.999 50.000 0.00 0.00 0.00 3.51
5531 6418 5.545658 ATCGTTGCAATATCGTTCTTGTT 57.454 34.783 0.59 0.00 0.00 2.83
5533 6420 6.031549 TGTATCGTTGCAATATCGTTCTTG 57.968 37.500 0.59 0.00 0.00 3.02
5542 6429 3.370672 CAGTGCACTGTATCGTTGCAATA 59.629 43.478 34.04 0.00 39.09 1.90
5550 6437 2.001872 TCAATGCAGTGCACTGTATCG 58.998 47.619 39.12 32.27 46.23 2.92
5554 6441 0.536687 AGCTCAATGCAGTGCACTGT 60.537 50.000 39.30 23.74 43.04 3.55
5561 6448 3.407424 TGTAGTCAAGCTCAATGCAGT 57.593 42.857 0.00 0.00 45.94 4.40
5579 6466 1.227999 CGCGTGAACTGGAACCATGT 61.228 55.000 0.00 0.00 0.00 3.21
5689 6576 0.250901 AAGACCGGAAGCTTGCACAT 60.251 50.000 18.65 1.91 0.00 3.21
5827 6731 0.109272 TTGGCTAAGCAGACTCGTCG 60.109 55.000 0.00 0.00 34.09 5.12
6017 6926 9.988815 CTGAGGCTATGTTTGATAGTAAAGTAT 57.011 33.333 0.00 0.00 0.00 2.12
6018 6927 8.978472 ACTGAGGCTATGTTTGATAGTAAAGTA 58.022 33.333 0.00 0.00 0.00 2.24
6019 6928 7.852263 ACTGAGGCTATGTTTGATAGTAAAGT 58.148 34.615 0.00 0.00 0.00 2.66
6020 6929 7.981789 TGACTGAGGCTATGTTTGATAGTAAAG 59.018 37.037 0.00 0.00 0.00 1.85
6021 6930 7.764443 GTGACTGAGGCTATGTTTGATAGTAAA 59.236 37.037 0.00 0.00 0.00 2.01
6022 6931 7.124298 AGTGACTGAGGCTATGTTTGATAGTAA 59.876 37.037 0.00 0.00 0.00 2.24
6023 6932 6.607600 AGTGACTGAGGCTATGTTTGATAGTA 59.392 38.462 0.00 0.00 0.00 1.82
6024 6933 5.423610 AGTGACTGAGGCTATGTTTGATAGT 59.576 40.000 0.00 0.00 0.00 2.12
6025 6934 5.911752 AGTGACTGAGGCTATGTTTGATAG 58.088 41.667 0.00 0.00 0.00 2.08
6026 6935 5.939764 AGTGACTGAGGCTATGTTTGATA 57.060 39.130 0.00 0.00 0.00 2.15
6027 6936 4.833478 AGTGACTGAGGCTATGTTTGAT 57.167 40.909 0.00 0.00 0.00 2.57
6028 6937 4.623932 AAGTGACTGAGGCTATGTTTGA 57.376 40.909 0.00 0.00 0.00 2.69
6029 6938 5.695851 AAAAGTGACTGAGGCTATGTTTG 57.304 39.130 0.00 0.00 0.00 2.93
6030 6939 9.515226 TTATAAAAAGTGACTGAGGCTATGTTT 57.485 29.630 0.00 0.00 0.00 2.83
6031 6940 8.947115 GTTATAAAAAGTGACTGAGGCTATGTT 58.053 33.333 0.00 0.00 0.00 2.71
6032 6941 8.100791 TGTTATAAAAAGTGACTGAGGCTATGT 58.899 33.333 0.00 0.00 0.00 2.29
6033 6942 8.492673 TGTTATAAAAAGTGACTGAGGCTATG 57.507 34.615 0.00 0.00 0.00 2.23
6034 6943 7.770897 CCTGTTATAAAAAGTGACTGAGGCTAT 59.229 37.037 0.00 0.00 0.00 2.97
6035 6944 7.038587 TCCTGTTATAAAAAGTGACTGAGGCTA 60.039 37.037 0.00 0.00 0.00 3.93
6036 6945 5.940470 CCTGTTATAAAAAGTGACTGAGGCT 59.060 40.000 0.00 0.00 0.00 4.58
6037 6946 5.938125 TCCTGTTATAAAAAGTGACTGAGGC 59.062 40.000 0.00 0.00 0.00 4.70
6038 6947 6.090898 CGTCCTGTTATAAAAAGTGACTGAGG 59.909 42.308 0.00 0.00 0.00 3.86
6039 6948 6.866770 TCGTCCTGTTATAAAAAGTGACTGAG 59.133 38.462 0.00 0.00 0.00 3.35
6040 6949 6.751157 TCGTCCTGTTATAAAAAGTGACTGA 58.249 36.000 0.00 0.18 0.00 3.41
6041 6950 6.866770 TCTCGTCCTGTTATAAAAAGTGACTG 59.133 38.462 0.00 0.00 0.00 3.51
6042 6951 6.989659 TCTCGTCCTGTTATAAAAAGTGACT 58.010 36.000 0.00 0.00 0.00 3.41
6043 6952 7.621633 GCTTCTCGTCCTGTTATAAAAAGTGAC 60.622 40.741 0.00 0.00 0.00 3.67
6072 6981 0.605589 CTATCGGAGGGCATGGAGAC 59.394 60.000 0.00 0.00 0.00 3.36
6078 6987 2.902608 TCCATTACTATCGGAGGGCAT 58.097 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.