Multiple sequence alignment - TraesCS1B01G170200

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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 TraesCS1B01G170200 chr1B 100.000 4263 0 0 1679 5941 302033848 302038110 0.000000e+00 7873.0
1 TraesCS1B01G170200 chr1B 100.000 1225 0 0 1 1225 302032170 302033394 0.000000e+00 2263.0
2 TraesCS1B01G170200 chr1B 94.198 586 29 5 5359 5941 153425985 153426568 0.000000e+00 889.0
3 TraesCS1B01G170200 chr1A 93.704 2335 107 20 3056 5375 264215772 264213463 0.000000e+00 3461.0
4 TraesCS1B01G170200 chr1A 96.396 888 23 7 1968 2855 264216650 264215772 0.000000e+00 1454.0
5 TraesCS1B01G170200 chr1A 91.862 811 43 9 384 1194 264218374 264217587 0.000000e+00 1110.0
6 TraesCS1B01G170200 chr1A 93.351 376 18 3 1 376 264218946 264218578 3.130000e-152 549.0
7 TraesCS1B01G170200 chr1A 89.899 297 24 5 1679 1971 264217072 264216778 1.560000e-100 377.0
8 TraesCS1B01G170200 chr1D 90.830 2290 112 35 3120 5375 206309053 206311278 0.000000e+00 2976.0
9 TraesCS1B01G170200 chr1D 92.946 1049 48 17 1679 2707 206307703 206308745 0.000000e+00 1504.0
10 TraesCS1B01G170200 chr1D 88.746 853 44 18 392 1207 206306828 206307665 0.000000e+00 996.0
11 TraesCS1B01G170200 chr1D 87.302 315 28 6 91 405 206305701 206306003 3.410000e-92 350.0
12 TraesCS1B01G170200 chr1D 96.000 150 4 1 2706 2855 206308788 206308935 5.950000e-60 243.0
13 TraesCS1B01G170200 chr4B 95.034 584 23 6 5360 5941 163833014 163832435 0.000000e+00 913.0
14 TraesCS1B01G170200 chr3B 95.312 576 24 3 5366 5940 300309849 300310422 0.000000e+00 911.0
15 TraesCS1B01G170200 chr3B 94.349 584 30 3 5359 5941 828079498 828078917 0.000000e+00 893.0
16 TraesCS1B01G170200 chr3B 94.511 583 22 6 5359 5940 480336680 480337253 0.000000e+00 891.0
17 TraesCS1B01G170200 chr6B 95.431 569 22 4 5375 5940 230769398 230768831 0.000000e+00 904.0
18 TraesCS1B01G170200 chr6B 95.271 571 21 4 5370 5940 680042985 680043549 0.000000e+00 900.0
19 TraesCS1B01G170200 chr6B 90.654 107 9 1 2538 2644 519222915 519222810 2.230000e-29 141.0
20 TraesCS1B01G170200 chr6B 100.000 28 0 0 3105 3132 166119757 166119784 1.100000e-02 52.8
21 TraesCS1B01G170200 chr5B 95.423 568 24 2 5373 5940 166706373 166706938 0.000000e+00 904.0
22 TraesCS1B01G170200 chr2A 94.027 586 30 5 5358 5941 721914699 721915281 0.000000e+00 883.0
23 TraesCS1B01G170200 chr5D 81.448 221 26 9 2539 2758 373930423 373930217 3.680000e-37 167.0
24 TraesCS1B01G170200 chr2B 89.720 107 10 1 2538 2644 672332051 672332156 1.040000e-27 135.0
25 TraesCS1B01G170200 chr6D 100.000 28 0 0 3105 3132 87468379 87468406 1.100000e-02 52.8
26 TraesCS1B01G170200 chr6A 100.000 28 0 0 3105 3132 105593708 105593735 1.100000e-02 52.8


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 TraesCS1B01G170200 chr1B 302032170 302038110 5940 False 5068.0 7873 100.0000 1 5941 2 chr1B.!!$F2 5940
1 TraesCS1B01G170200 chr1B 153425985 153426568 583 False 889.0 889 94.1980 5359 5941 1 chr1B.!!$F1 582
2 TraesCS1B01G170200 chr1A 264213463 264218946 5483 True 1390.2 3461 93.0424 1 5375 5 chr1A.!!$R1 5374
3 TraesCS1B01G170200 chr1D 206305701 206311278 5577 False 1213.8 2976 91.1648 91 5375 5 chr1D.!!$F1 5284
4 TraesCS1B01G170200 chr4B 163832435 163833014 579 True 913.0 913 95.0340 5360 5941 1 chr4B.!!$R1 581
5 TraesCS1B01G170200 chr3B 300309849 300310422 573 False 911.0 911 95.3120 5366 5940 1 chr3B.!!$F1 574
6 TraesCS1B01G170200 chr3B 828078917 828079498 581 True 893.0 893 94.3490 5359 5941 1 chr3B.!!$R1 582
7 TraesCS1B01G170200 chr3B 480336680 480337253 573 False 891.0 891 94.5110 5359 5940 1 chr3B.!!$F2 581
8 TraesCS1B01G170200 chr6B 230768831 230769398 567 True 904.0 904 95.4310 5375 5940 1 chr6B.!!$R1 565
9 TraesCS1B01G170200 chr6B 680042985 680043549 564 False 900.0 900 95.2710 5370 5940 1 chr6B.!!$F2 570
10 TraesCS1B01G170200 chr5B 166706373 166706938 565 False 904.0 904 95.4230 5373 5940 1 chr5B.!!$F1 567
11 TraesCS1B01G170200 chr2A 721914699 721915281 582 False 883.0 883 94.0270 5358 5941 1 chr2A.!!$F1 583

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
654 1686 1.519013 GCGCCCGTTACGGTTATGA 60.519 57.895 22.78 0.00 46.80 2.15 F
855 1938 3.200593 GGTCCTCGCGTCGCTCTA 61.201 66.667 16.36 0.00 0.00 2.43 F
990 2074 3.354089 TTTCTGCTTGCAACACTTAGC 57.646 42.857 0.00 0.00 0.00 3.09 F
2864 4618 0.031994 AACATTCAGTTGTTGGCGCC 59.968 50.000 22.73 22.73 39.49 6.53 F
4071 5898 0.109781 GGGCGCAGTATTTGTGTGTG 60.110 55.000 10.83 0.00 39.53 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 3456 0.324830 GGAGGGAGTAGAGCAGTGGT 60.325 60.0 0.00 0.0 0.00 4.16 R
1912 3463 2.649531 ATGAGACGGAGGGAGTAGAG 57.350 55.0 0.00 0.0 0.00 2.43 R
2895 4649 0.251386 AGGAGAGAGTTCAGTGCGGA 60.251 55.0 0.00 0.0 0.00 5.54 R
4811 6662 0.179097 GACAGTCGATGAAGGCCTCC 60.179 60.0 5.23 0.0 0.00 4.30 R
5066 6921 0.180406 ACAAGTCGCAACTCCCAACT 59.820 50.0 0.00 0.0 33.48 3.16 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
33 34 4.202493 TGAGAATCCACCCATCACATATGG 60.202 45.833 7.80 0.00 38.88 2.74
71 72 2.158871 GGGCCCGTCACATATGTCTTTA 60.159 50.000 5.69 0.00 0.00 1.85
83 84 7.395772 TCACATATGTCTTTAAGCCCAAAATCA 59.604 33.333 5.07 0.00 0.00 2.57
128 129 6.872920 AGTGAGACCAAGTTTGCAATTTTAA 58.127 32.000 0.00 0.00 0.00 1.52
129 130 7.500141 AGTGAGACCAAGTTTGCAATTTTAAT 58.500 30.769 0.00 0.00 0.00 1.40
130 131 7.986889 AGTGAGACCAAGTTTGCAATTTTAATT 59.013 29.630 0.00 0.00 0.00 1.40
131 132 9.255304 GTGAGACCAAGTTTGCAATTTTAATTA 57.745 29.630 0.00 0.00 0.00 1.40
163 164 6.036577 TGAAGGGCCAAAATCATACTTTTC 57.963 37.500 6.18 0.00 0.00 2.29
335 336 3.051581 AGGGCTCATCACATCCATTACT 58.948 45.455 0.00 0.00 0.00 2.24
363 364 4.895224 ACGTGGACTTCCTTTTCTTTTC 57.105 40.909 0.00 0.00 36.82 2.29
433 1465 7.904558 ACAGAAGTAGGTGAGATCATATTCA 57.095 36.000 0.00 0.00 0.00 2.57
439 1471 5.627182 AGGTGAGATCATATTCAACTGCT 57.373 39.130 0.00 0.00 39.77 4.24
440 1472 5.999044 AGGTGAGATCATATTCAACTGCTT 58.001 37.500 0.00 0.00 39.77 3.91
466 1498 4.956075 AGCCTTCTCCTTTGACAAGAAAAA 59.044 37.500 0.00 0.00 30.57 1.94
483 1515 9.174166 ACAAGAAAAATTAGCCTCGTTATATGT 57.826 29.630 0.00 0.00 0.00 2.29
488 1520 8.902540 AAAATTAGCCTCGTTATATGTCATCA 57.097 30.769 0.00 0.00 0.00 3.07
498 1530 8.687292 TCGTTATATGTCATCACCTACTTACT 57.313 34.615 0.00 0.00 0.00 2.24
596 1628 2.764439 ACTAAAGAGGAGCCGAAACC 57.236 50.000 0.00 0.00 0.00 3.27
654 1686 1.519013 GCGCCCGTTACGGTTATGA 60.519 57.895 22.78 0.00 46.80 2.15
701 1755 8.058328 CGTATTGAGCATAGATACTTTGTGTTG 58.942 37.037 0.00 0.00 0.00 3.33
702 1756 7.928307 ATTGAGCATAGATACTTTGTGTTGT 57.072 32.000 0.00 0.00 0.00 3.32
704 1758 8.840833 TTGAGCATAGATACTTTGTGTTGTAA 57.159 30.769 0.00 0.00 0.00 2.41
705 1759 8.251750 TGAGCATAGATACTTTGTGTTGTAAC 57.748 34.615 0.00 0.00 0.00 2.50
706 1760 8.094548 TGAGCATAGATACTTTGTGTTGTAACT 58.905 33.333 0.00 0.00 0.00 2.24
707 1761 8.256611 AGCATAGATACTTTGTGTTGTAACTG 57.743 34.615 0.00 0.00 0.00 3.16
708 1762 7.878127 AGCATAGATACTTTGTGTTGTAACTGT 59.122 33.333 0.00 0.00 0.00 3.55
709 1763 9.146984 GCATAGATACTTTGTGTTGTAACTGTA 57.853 33.333 0.00 0.00 0.00 2.74
780 1836 9.615295 GTTTAAAAGCGTAGGAAATTCAACATA 57.385 29.630 0.00 0.00 0.00 2.29
808 1891 6.127026 CCAGCCTATAACCTTCAGAAACTAGT 60.127 42.308 0.00 0.00 0.00 2.57
855 1938 3.200593 GGTCCTCGCGTCGCTCTA 61.201 66.667 16.36 0.00 0.00 2.43
983 2067 3.911661 AGAGTCATTTCTGCTTGCAAC 57.088 42.857 0.00 0.00 0.00 4.17
990 2074 3.354089 TTTCTGCTTGCAACACTTAGC 57.646 42.857 0.00 0.00 0.00 3.09
1222 2773 8.997301 AGGATTATACTCCCTTCATTCCTAAT 57.003 34.615 5.53 0.00 35.79 1.73
1817 3368 3.673484 GCCATGCGTTGCAGTGGT 61.673 61.111 16.20 0.00 43.65 4.16
1830 3381 5.738693 CGTTGCAGTGGTGACATAAATATTG 59.261 40.000 0.00 0.00 46.14 1.90
1836 3387 9.104965 GCAGTGGTGACATAAATATTGTAGTAA 57.895 33.333 0.00 0.00 46.14 2.24
1898 3449 5.245531 TCACTCCACTGAACCATTGAATAC 58.754 41.667 0.00 0.00 0.00 1.89
1899 3450 4.396166 CACTCCACTGAACCATTGAATACC 59.604 45.833 0.00 0.00 0.00 2.73
1900 3451 4.042809 ACTCCACTGAACCATTGAATACCA 59.957 41.667 0.00 0.00 0.00 3.25
1901 3452 4.588899 TCCACTGAACCATTGAATACCAG 58.411 43.478 0.00 0.00 0.00 4.00
1902 3453 4.042809 TCCACTGAACCATTGAATACCAGT 59.957 41.667 0.00 0.00 34.17 4.00
1903 3454 5.249622 TCCACTGAACCATTGAATACCAGTA 59.750 40.000 0.00 0.00 32.81 2.74
1904 3455 6.069673 TCCACTGAACCATTGAATACCAGTAT 60.070 38.462 0.00 0.00 32.81 2.12
1905 3456 7.126573 TCCACTGAACCATTGAATACCAGTATA 59.873 37.037 0.00 0.00 32.81 1.47
2039 3746 2.749621 CCCAACCTTGAGCATTGTACTC 59.250 50.000 0.00 0.00 34.62 2.59
2230 3937 2.722094 TCCTTTATCCATGCACACACC 58.278 47.619 0.00 0.00 0.00 4.16
2279 3987 4.690261 GGAGAGGATGTCCTTCAGCTACTA 60.690 50.000 2.55 0.00 46.84 1.82
2302 4010 8.573885 ACTAAAACCAAAAGAAGCTTGTATACC 58.426 33.333 2.10 0.00 0.00 2.73
2521 4230 2.093310 CACTATCACTGCGCTTCAACAG 59.907 50.000 9.73 0.00 39.86 3.16
2669 4378 6.294176 CCACCACAGAAGTATTTTCTTTCCTG 60.294 42.308 0.00 0.00 0.00 3.86
2855 4609 6.699575 AAGTTCAGCTTACAACATTCAGTT 57.300 33.333 3.43 0.00 36.89 3.16
2863 4617 3.568093 AACATTCAGTTGTTGGCGC 57.432 47.368 0.00 0.00 39.49 6.53
2864 4618 0.031994 AACATTCAGTTGTTGGCGCC 59.968 50.000 22.73 22.73 39.49 6.53
2865 4619 1.442520 CATTCAGTTGTTGGCGCCG 60.443 57.895 23.90 5.27 0.00 6.46
2866 4620 3.267597 ATTCAGTTGTTGGCGCCGC 62.268 57.895 23.90 17.91 0.00 6.53
2892 4646 3.426568 GCAGCGCCGCTTCTTCTT 61.427 61.111 9.89 0.00 36.40 2.52
2893 4647 2.781300 CAGCGCCGCTTCTTCTTC 59.219 61.111 9.89 0.00 36.40 2.87
2894 4648 1.739562 CAGCGCCGCTTCTTCTTCT 60.740 57.895 9.89 0.00 36.40 2.85
2895 4649 1.004440 AGCGCCGCTTCTTCTTCTT 60.004 52.632 5.39 0.00 33.89 2.52
2896 4650 1.016653 AGCGCCGCTTCTTCTTCTTC 61.017 55.000 5.39 0.00 33.89 2.87
2897 4651 1.972027 GCGCCGCTTCTTCTTCTTCC 61.972 60.000 0.00 0.00 0.00 3.46
2898 4652 1.687494 CGCCGCTTCTTCTTCTTCCG 61.687 60.000 0.00 0.00 0.00 4.30
2899 4653 1.972027 GCCGCTTCTTCTTCTTCCGC 61.972 60.000 0.00 0.00 0.00 5.54
2900 4654 0.670546 CCGCTTCTTCTTCTTCCGCA 60.671 55.000 0.00 0.00 0.00 5.69
2901 4655 0.440371 CGCTTCTTCTTCTTCCGCAC 59.560 55.000 0.00 0.00 0.00 5.34
2902 4656 1.802069 GCTTCTTCTTCTTCCGCACT 58.198 50.000 0.00 0.00 0.00 4.40
2903 4657 1.462670 GCTTCTTCTTCTTCCGCACTG 59.537 52.381 0.00 0.00 0.00 3.66
2904 4658 2.868044 GCTTCTTCTTCTTCCGCACTGA 60.868 50.000 0.00 0.00 0.00 3.41
2905 4659 3.393800 CTTCTTCTTCTTCCGCACTGAA 58.606 45.455 0.00 0.00 0.00 3.02
2906 4660 2.755650 TCTTCTTCTTCCGCACTGAAC 58.244 47.619 0.00 0.00 0.00 3.18
2907 4661 2.365617 TCTTCTTCTTCCGCACTGAACT 59.634 45.455 0.00 0.00 0.00 3.01
2908 4662 2.440539 TCTTCTTCCGCACTGAACTC 57.559 50.000 0.00 0.00 0.00 3.01
2909 4663 1.964223 TCTTCTTCCGCACTGAACTCT 59.036 47.619 0.00 0.00 0.00 3.24
2910 4664 2.029828 TCTTCTTCCGCACTGAACTCTC 60.030 50.000 0.00 0.00 0.00 3.20
2911 4665 1.621992 TCTTCCGCACTGAACTCTCT 58.378 50.000 0.00 0.00 0.00 3.10
2912 4666 1.542030 TCTTCCGCACTGAACTCTCTC 59.458 52.381 0.00 0.00 0.00 3.20
2913 4667 0.603569 TTCCGCACTGAACTCTCTCC 59.396 55.000 0.00 0.00 0.00 3.71
2914 4668 0.251386 TCCGCACTGAACTCTCTCCT 60.251 55.000 0.00 0.00 0.00 3.69
2915 4669 0.605589 CCGCACTGAACTCTCTCCTT 59.394 55.000 0.00 0.00 0.00 3.36
2916 4670 1.001406 CCGCACTGAACTCTCTCCTTT 59.999 52.381 0.00 0.00 0.00 3.11
2917 4671 2.333014 CGCACTGAACTCTCTCCTTTC 58.667 52.381 0.00 0.00 0.00 2.62
2918 4672 2.029470 CGCACTGAACTCTCTCCTTTCT 60.029 50.000 0.00 0.00 0.00 2.52
2919 4673 3.553922 CGCACTGAACTCTCTCCTTTCTT 60.554 47.826 0.00 0.00 0.00 2.52
2920 4674 4.384940 GCACTGAACTCTCTCCTTTCTTT 58.615 43.478 0.00 0.00 0.00 2.52
2921 4675 4.213059 GCACTGAACTCTCTCCTTTCTTTG 59.787 45.833 0.00 0.00 0.00 2.77
2922 4676 5.363939 CACTGAACTCTCTCCTTTCTTTGT 58.636 41.667 0.00 0.00 0.00 2.83
2923 4677 5.465056 CACTGAACTCTCTCCTTTCTTTGTC 59.535 44.000 0.00 0.00 0.00 3.18
2924 4678 5.365314 ACTGAACTCTCTCCTTTCTTTGTCT 59.635 40.000 0.00 0.00 0.00 3.41
2925 4679 6.126911 ACTGAACTCTCTCCTTTCTTTGTCTT 60.127 38.462 0.00 0.00 0.00 3.01
2926 4680 6.284459 TGAACTCTCTCCTTTCTTTGTCTTC 58.716 40.000 0.00 0.00 0.00 2.87
2927 4681 6.098982 TGAACTCTCTCCTTTCTTTGTCTTCT 59.901 38.462 0.00 0.00 0.00 2.85
2928 4682 6.096673 ACTCTCTCCTTTCTTTGTCTTCTC 57.903 41.667 0.00 0.00 0.00 2.87
2929 4683 5.838521 ACTCTCTCCTTTCTTTGTCTTCTCT 59.161 40.000 0.00 0.00 0.00 3.10
2930 4684 6.015434 ACTCTCTCCTTTCTTTGTCTTCTCTC 60.015 42.308 0.00 0.00 0.00 3.20
2931 4685 5.835819 TCTCTCCTTTCTTTGTCTTCTCTCA 59.164 40.000 0.00 0.00 0.00 3.27
2932 4686 6.325028 TCTCTCCTTTCTTTGTCTTCTCTCAA 59.675 38.462 0.00 0.00 0.00 3.02
2933 4687 6.520272 TCTCCTTTCTTTGTCTTCTCTCAAG 58.480 40.000 0.00 0.00 0.00 3.02
2934 4688 6.325028 TCTCCTTTCTTTGTCTTCTCTCAAGA 59.675 38.462 0.00 0.00 0.00 3.02
2935 4689 6.889198 TCCTTTCTTTGTCTTCTCTCAAGAA 58.111 36.000 0.00 0.00 39.22 2.52
2936 4690 6.763610 TCCTTTCTTTGTCTTCTCTCAAGAAC 59.236 38.462 0.00 0.00 36.59 3.01
2937 4691 6.540189 CCTTTCTTTGTCTTCTCTCAAGAACA 59.460 38.462 0.00 0.00 36.59 3.18
2938 4692 6.910536 TTCTTTGTCTTCTCTCAAGAACAC 57.089 37.500 0.00 0.00 36.59 3.32
2939 4693 5.977635 TCTTTGTCTTCTCTCAAGAACACA 58.022 37.500 0.00 0.00 38.26 3.72
2940 4694 5.812642 TCTTTGTCTTCTCTCAAGAACACAC 59.187 40.000 0.00 0.00 39.29 3.82
2941 4695 4.736126 TGTCTTCTCTCAAGAACACACA 57.264 40.909 0.00 0.00 36.05 3.72
2942 4696 4.433615 TGTCTTCTCTCAAGAACACACAC 58.566 43.478 0.00 0.00 36.05 3.82
2943 4697 4.081697 TGTCTTCTCTCAAGAACACACACA 60.082 41.667 0.00 0.00 36.05 3.72
2944 4698 4.268884 GTCTTCTCTCAAGAACACACACAC 59.731 45.833 0.00 0.00 36.59 3.82
2945 4699 3.885724 TCTCTCAAGAACACACACACA 57.114 42.857 0.00 0.00 0.00 3.72
2946 4700 3.521560 TCTCTCAAGAACACACACACAC 58.478 45.455 0.00 0.00 0.00 3.82
2947 4701 2.267426 TCTCAAGAACACACACACACG 58.733 47.619 0.00 0.00 0.00 4.49
2948 4702 0.724549 TCAAGAACACACACACACGC 59.275 50.000 0.00 0.00 0.00 5.34
2949 4703 0.445829 CAAGAACACACACACACGCA 59.554 50.000 0.00 0.00 0.00 5.24
2950 4704 0.446222 AAGAACACACACACACGCAC 59.554 50.000 0.00 0.00 0.00 5.34
2951 4705 0.672091 AGAACACACACACACGCACA 60.672 50.000 0.00 0.00 0.00 4.57
2952 4706 0.520412 GAACACACACACACGCACAC 60.520 55.000 0.00 0.00 0.00 3.82
2954 4708 3.860125 ACACACACACGCACACGC 61.860 61.111 0.00 0.00 45.53 5.34
2955 4709 3.858989 CACACACACGCACACGCA 61.859 61.111 0.00 0.00 45.53 5.24
2956 4710 3.860125 ACACACACGCACACGCAC 61.860 61.111 0.00 0.00 45.53 5.34
2957 4711 3.858989 CACACACGCACACGCACA 61.859 61.111 0.00 0.00 45.53 4.57
2958 4712 3.860125 ACACACGCACACGCACAC 61.860 61.111 0.00 0.00 45.53 3.82
2959 4713 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
3021 4775 3.858989 CGCGCACACACACACACA 61.859 61.111 8.75 0.00 0.00 3.72
3022 4776 2.277247 GCGCACACACACACACAC 60.277 61.111 0.30 0.00 0.00 3.82
3023 4777 3.033166 GCGCACACACACACACACA 62.033 57.895 0.30 0.00 0.00 3.72
3024 4778 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
3025 4779 1.872468 GCACACACACACACACACA 59.128 52.632 0.00 0.00 0.00 3.72
3026 4780 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
3027 4781 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3028 4782 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
3029 4783 1.265635 ACACACACACACACACACAAC 59.734 47.619 0.00 0.00 0.00 3.32
3030 4784 1.265365 CACACACACACACACACAACA 59.735 47.619 0.00 0.00 0.00 3.33
3031 4785 1.265635 ACACACACACACACACAACAC 59.734 47.619 0.00 0.00 0.00 3.32
3032 4786 1.265365 CACACACACACACACAACACA 59.735 47.619 0.00 0.00 0.00 3.72
3033 4787 2.095314 CACACACACACACACAACACAT 60.095 45.455 0.00 0.00 0.00 3.21
3034 4788 2.095314 ACACACACACACACAACACATG 60.095 45.455 0.00 0.00 0.00 3.21
3035 4789 2.161211 CACACACACACACAACACATGA 59.839 45.455 0.00 0.00 0.00 3.07
3036 4790 3.016031 ACACACACACACAACACATGAT 58.984 40.909 0.00 0.00 0.00 2.45
3037 4791 3.181498 ACACACACACACAACACATGATG 60.181 43.478 0.00 0.00 0.00 3.07
3038 4792 3.065095 CACACACACACAACACATGATGA 59.935 43.478 0.00 0.00 0.00 2.92
3039 4793 3.693578 ACACACACACAACACATGATGAA 59.306 39.130 0.00 0.00 0.00 2.57
3040 4794 4.157472 ACACACACACAACACATGATGAAA 59.843 37.500 0.00 0.00 0.00 2.69
3041 4795 4.736307 CACACACACAACACATGATGAAAG 59.264 41.667 0.00 0.00 0.00 2.62
3042 4796 3.732219 CACACACAACACATGATGAAAGC 59.268 43.478 0.00 0.00 0.00 3.51
3043 4797 3.243501 ACACACAACACATGATGAAAGCC 60.244 43.478 0.00 0.00 0.00 4.35
3044 4798 2.957680 ACACAACACATGATGAAAGCCA 59.042 40.909 0.00 0.00 0.00 4.75
3045 4799 3.005050 ACACAACACATGATGAAAGCCAG 59.995 43.478 0.00 0.00 0.00 4.85
3046 4800 2.559668 ACAACACATGATGAAAGCCAGG 59.440 45.455 0.00 0.00 0.00 4.45
3047 4801 2.559668 CAACACATGATGAAAGCCAGGT 59.440 45.455 0.00 0.00 0.00 4.00
3048 4802 2.165167 ACACATGATGAAAGCCAGGTG 58.835 47.619 0.00 0.00 46.60 4.00
3049 4803 2.165167 CACATGATGAAAGCCAGGTGT 58.835 47.619 0.00 0.00 39.40 4.16
3050 4804 2.163010 CACATGATGAAAGCCAGGTGTC 59.837 50.000 0.00 0.00 39.40 3.67
3051 4805 2.224843 ACATGATGAAAGCCAGGTGTCA 60.225 45.455 0.00 0.00 0.00 3.58
3052 4806 2.885135 TGATGAAAGCCAGGTGTCAT 57.115 45.000 2.17 2.17 33.45 3.06
3053 4807 2.439409 TGATGAAAGCCAGGTGTCATG 58.561 47.619 7.23 0.00 30.94 3.07
3054 4808 2.224843 TGATGAAAGCCAGGTGTCATGT 60.225 45.455 7.23 0.00 30.94 3.21
3055 4809 2.363306 TGAAAGCCAGGTGTCATGTT 57.637 45.000 0.00 0.00 0.00 2.71
3065 4819 2.158623 AGGTGTCATGTTCTCCAAGCAA 60.159 45.455 11.77 0.00 0.00 3.91
3081 4835 5.649395 TCCAAGCAATCCTCTTAATTGAGTG 59.351 40.000 0.00 0.00 36.43 3.51
3149 4946 4.173256 ACGGCAAAATAAAATACTGCAGC 58.827 39.130 15.27 0.00 34.66 5.25
3167 4964 1.202417 AGCGATGTAGATCAACCCACG 60.202 52.381 0.29 0.00 0.00 4.94
3169 4966 2.888594 CGATGTAGATCAACCCACGTT 58.111 47.619 0.29 0.00 0.00 3.99
3201 4999 4.523173 ACGACTGACTTTGACAAGATCCTA 59.477 41.667 0.00 0.00 33.72 2.94
3296 5106 3.809832 CGAGGGCTGAATTATACACCTTG 59.190 47.826 0.00 0.00 0.00 3.61
3413 5223 1.153628 GCTACATGTTCCGGCGACT 60.154 57.895 9.30 0.00 0.00 4.18
3437 5247 4.754372 CAGACTTGCTGCAAAGACAATA 57.246 40.909 16.74 0.00 37.90 1.90
3510 5320 7.463544 TGTGAATCGTTAATGCTAATCAACTG 58.536 34.615 0.00 0.00 0.00 3.16
3530 5340 4.042809 ACTGACCCAATCACTTCATACCAA 59.957 41.667 0.00 0.00 32.37 3.67
3579 5392 1.134189 GCCCACAGAACCTACATACCC 60.134 57.143 0.00 0.00 0.00 3.69
3600 5413 3.236816 CTGTAGCAAAATCTTTGCCACG 58.763 45.455 17.99 9.28 45.98 4.94
3603 5416 0.319813 GCAAAATCTTTGCCACGCCT 60.320 50.000 12.10 0.00 39.38 5.52
3604 5417 1.067915 GCAAAATCTTTGCCACGCCTA 60.068 47.619 12.10 0.00 39.38 3.93
3605 5418 2.609244 GCAAAATCTTTGCCACGCCTAA 60.609 45.455 12.10 0.00 39.38 2.69
3606 5419 3.648009 CAAAATCTTTGCCACGCCTAAA 58.352 40.909 0.00 0.00 0.00 1.85
3700 5521 3.459027 CGCTTGAGCTCGCGTTAA 58.541 55.556 22.87 5.67 44.01 2.01
3771 5592 4.702081 GCTCTGCGTCGTCCGTGT 62.702 66.667 0.00 0.00 39.32 4.49
3772 5593 2.050351 CTCTGCGTCGTCCGTGTT 60.050 61.111 0.00 0.00 39.32 3.32
3932 5759 0.742281 GCTCAGCTGGATCGCTTGAA 60.742 55.000 15.13 0.00 38.41 2.69
3974 5801 2.750237 GTTCGGCAGCGGGGATTT 60.750 61.111 0.00 0.00 0.00 2.17
3976 5803 2.966732 TTCGGCAGCGGGGATTTCT 61.967 57.895 0.00 0.00 0.00 2.52
4061 5888 2.579201 GCAGAGAAGGGCGCAGTA 59.421 61.111 10.83 0.00 0.00 2.74
4064 5891 2.014068 GCAGAGAAGGGCGCAGTATTT 61.014 52.381 10.83 0.00 0.00 1.40
4065 5892 1.667724 CAGAGAAGGGCGCAGTATTTG 59.332 52.381 10.83 0.00 0.00 2.32
4066 5893 1.279271 AGAGAAGGGCGCAGTATTTGT 59.721 47.619 10.83 0.00 0.00 2.83
4067 5894 1.398390 GAGAAGGGCGCAGTATTTGTG 59.602 52.381 10.83 0.00 40.33 3.33
4068 5895 1.165270 GAAGGGCGCAGTATTTGTGT 58.835 50.000 10.83 0.00 39.53 3.72
4069 5896 0.881118 AAGGGCGCAGTATTTGTGTG 59.119 50.000 10.83 0.00 39.53 3.82
4070 5897 0.250727 AGGGCGCAGTATTTGTGTGT 60.251 50.000 10.83 0.00 39.53 3.72
4071 5898 0.109781 GGGCGCAGTATTTGTGTGTG 60.110 55.000 10.83 0.00 39.53 3.82
4072 5899 0.591170 GGCGCAGTATTTGTGTGTGT 59.409 50.000 10.83 0.00 39.53 3.72
4073 5900 1.662876 GGCGCAGTATTTGTGTGTGTG 60.663 52.381 10.83 0.00 39.53 3.82
4074 5901 1.002900 GCGCAGTATTTGTGTGTGTGT 60.003 47.619 0.30 0.00 39.53 3.72
4075 5902 2.638673 CGCAGTATTTGTGTGTGTGTG 58.361 47.619 0.00 0.00 32.55 3.82
4120 5967 7.558807 TCTTGTTAGACACCGGAGAGATTATAA 59.441 37.037 9.46 0.00 0.00 0.98
4150 5997 4.648651 TCGTATCTCTCAATCCGGTATCA 58.351 43.478 0.00 0.00 0.00 2.15
4277 6128 0.618107 TGCCCAAGTACGGATACCCA 60.618 55.000 0.00 0.00 30.88 4.51
4335 6186 0.384725 CTTGTCGCTGAACAAAGCCG 60.385 55.000 0.00 0.00 40.23 5.52
4350 6201 1.086067 AGCCGTCGTGAGATGCAATG 61.086 55.000 0.00 0.00 45.72 2.82
4446 6297 1.331756 GCATGCAGTAGCGCAGTAATT 59.668 47.619 14.21 0.00 46.99 1.40
4490 6341 5.738783 GCTGGAGCCAATTGAAAACAACTTA 60.739 40.000 7.12 0.00 34.31 2.24
4511 6362 3.508845 AACCACTACTGGAGCAACATT 57.491 42.857 0.00 0.00 40.55 2.71
4610 6461 2.656069 GGACTACTTCAGGGCCGCA 61.656 63.158 0.00 0.00 0.00 5.69
4793 6644 2.962421 GCAGCTCTACCAGATCTACCTT 59.038 50.000 0.00 0.00 0.00 3.50
4811 6662 1.492319 TTTGCGTCGACAAGAACGGG 61.492 55.000 17.16 0.00 0.00 5.28
4932 6783 1.548081 CAAGATCATGTTGCCCACCA 58.452 50.000 0.00 0.00 0.00 4.17
4954 6805 2.930019 CTGAGAGCCACCCACCCA 60.930 66.667 0.00 0.00 0.00 4.51
5020 6871 1.290203 ATATCGTGCTTGTTGCTCCG 58.710 50.000 0.00 0.00 43.37 4.63
5091 6946 2.415512 GGGAGTTGCGACTTGTCATAAC 59.584 50.000 8.34 5.55 35.88 1.89
5142 6997 8.380743 ACTAGCTACTATGTATATGCGTATCC 57.619 38.462 0.55 0.00 0.00 2.59
5215 7072 9.908152 CGGGTGTTTAAGAAATTCTTTTATCTT 57.092 29.630 13.89 0.00 37.89 2.40
5224 7081 9.678941 AAGAAATTCTTTTATCTTGGTTCGTTC 57.321 29.630 1.80 0.00 31.57 3.95
5251 7109 1.985473 TTGTTCATGGCTGCTTCTGT 58.015 45.000 0.00 0.00 0.00 3.41
5257 7115 1.610038 CATGGCTGCTTCTGTTGTTGA 59.390 47.619 0.00 0.00 0.00 3.18
5293 7151 9.304731 GTTTCAAATTTAGTTTCCCGTAAGTTT 57.695 29.630 0.00 0.00 0.00 2.66
5310 7168 8.404000 CCGTAAGTTTGACTACATACAGTCTAT 58.596 37.037 5.00 0.00 44.41 1.98
5311 7169 9.222916 CGTAAGTTTGACTACATACAGTCTATG 57.777 37.037 5.00 0.00 44.41 2.23
5319 7177 9.286170 TGACTACATACAGTCTATGAGTTATCC 57.714 37.037 5.00 0.00 44.41 2.59
5341 7199 3.523606 TTTGTTTGTGCTTCAGTGCAT 57.476 38.095 0.00 0.00 45.23 3.96
5342 7200 2.495409 TGTTTGTGCTTCAGTGCATG 57.505 45.000 0.00 0.00 45.23 4.06
5343 7201 1.067364 TGTTTGTGCTTCAGTGCATGG 59.933 47.619 0.00 0.00 45.23 3.66
5347 7206 1.755959 TGTGCTTCAGTGCATGGTTTT 59.244 42.857 0.00 0.00 45.23 2.43
5414 7276 0.941542 TTGCAACGGGAGAGAAAACG 59.058 50.000 0.00 0.00 0.00 3.60
5485 7347 5.513141 GTCCATCTCTTTTATTTTTGCGAGC 59.487 40.000 0.00 0.00 0.00 5.03
5694 7562 4.911610 CGCGATGAGAAATCTGTTGTTTTT 59.088 37.500 0.00 0.00 0.00 1.94
5699 7567 7.324616 CGATGAGAAATCTGTTGTTTTTCCTTC 59.675 37.037 0.00 0.00 31.25 3.46
5715 7583 3.074412 TCCTTCCGACATTTTTCAGAGC 58.926 45.455 0.00 0.00 0.00 4.09
5783 7653 9.647918 TTATAGTGGGGTATTTATTTGCAATCA 57.352 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.547372 GCCCCATCACATATGCAATCC 59.453 52.381 1.58 0.00 0.00 3.01
36 37 0.469705 GGGCCCCATCACATATGCAA 60.470 55.000 12.23 0.00 0.00 4.08
71 72 2.299867 GGTCATGTGTGATTTTGGGCTT 59.700 45.455 0.00 0.00 36.60 4.35
128 129 3.238597 TGGCCCTTCAAGTTTTGCTAAT 58.761 40.909 0.00 0.00 0.00 1.73
129 130 2.672098 TGGCCCTTCAAGTTTTGCTAA 58.328 42.857 0.00 0.00 0.00 3.09
130 131 2.373335 TGGCCCTTCAAGTTTTGCTA 57.627 45.000 0.00 0.00 0.00 3.49
131 132 1.494960 TTGGCCCTTCAAGTTTTGCT 58.505 45.000 0.00 0.00 0.00 3.91
138 139 5.665916 AAGTATGATTTTGGCCCTTCAAG 57.334 39.130 0.00 0.00 0.00 3.02
163 164 2.513738 TCAGGACCTATTTGGATTGGGG 59.486 50.000 0.00 0.00 39.71 4.96
298 299 2.304761 AGCCCTCGAAACCTAATGTCAA 59.695 45.455 0.00 0.00 0.00 3.18
299 300 1.906574 AGCCCTCGAAACCTAATGTCA 59.093 47.619 0.00 0.00 0.00 3.58
303 304 2.771943 TGATGAGCCCTCGAAACCTAAT 59.228 45.455 0.00 0.00 0.00 1.73
335 336 3.564053 AAGGAAGTCCACGTAAAACCA 57.436 42.857 0.00 0.00 38.89 3.67
363 364 8.110860 ACCAGAGTTTTTGTTACCATTATCTG 57.889 34.615 0.00 0.00 0.00 2.90
416 1448 6.737720 AGCAGTTGAATATGATCTCACCTA 57.262 37.500 0.00 0.00 0.00 3.08
428 1460 3.055819 AGAAGGCTCGAAGCAGTTGAATA 60.056 43.478 8.71 0.00 44.75 1.75
429 1461 2.079925 GAAGGCTCGAAGCAGTTGAAT 58.920 47.619 8.71 0.00 44.75 2.57
430 1462 1.070758 AGAAGGCTCGAAGCAGTTGAA 59.929 47.619 8.71 0.00 44.75 2.69
433 1465 0.036858 GGAGAAGGCTCGAAGCAGTT 60.037 55.000 8.71 2.48 44.75 3.16
439 1471 1.691976 TGTCAAAGGAGAAGGCTCGAA 59.308 47.619 0.00 0.00 42.25 3.71
440 1472 1.338107 TGTCAAAGGAGAAGGCTCGA 58.662 50.000 0.00 0.00 42.25 4.04
466 1498 6.211584 AGGTGATGACATATAACGAGGCTAAT 59.788 38.462 0.00 0.00 0.00 1.73
483 1515 8.851145 GTGATGATCTAAGTAAGTAGGTGATGA 58.149 37.037 0.00 0.00 0.00 2.92
551 1583 2.634453 GGCCCCATATTTTGCTTATGCT 59.366 45.455 0.00 0.00 40.48 3.79
557 1589 2.501316 GTTTCTGGCCCCATATTTTGCT 59.499 45.455 0.00 0.00 0.00 3.91
558 1590 2.501316 AGTTTCTGGCCCCATATTTTGC 59.499 45.455 0.00 0.00 0.00 3.68
596 1628 4.396854 GTAGCGGCCACTACTTCG 57.603 61.111 21.37 0.00 39.57 3.79
654 1686 3.497227 CGATCGGGGTATGGGGTTAAATT 60.497 47.826 7.38 0.00 0.00 1.82
718 1772 9.478768 TCAACAAAATAAGACGTGTCTAACATA 57.521 29.630 2.42 0.00 39.39 2.29
719 1773 8.373048 TCAACAAAATAAGACGTGTCTAACAT 57.627 30.769 2.42 0.00 39.39 2.71
720 1774 7.493320 ACTCAACAAAATAAGACGTGTCTAACA 59.507 33.333 2.42 0.00 39.39 2.41
721 1775 7.848491 ACTCAACAAAATAAGACGTGTCTAAC 58.152 34.615 2.42 0.00 39.39 2.34
722 1776 8.428186 AACTCAACAAAATAAGACGTGTCTAA 57.572 30.769 2.42 0.00 39.39 2.10
723 1777 9.701098 ATAACTCAACAAAATAAGACGTGTCTA 57.299 29.630 2.42 0.00 39.39 2.59
724 1778 6.920569 AACTCAACAAAATAAGACGTGTCT 57.079 33.333 0.00 0.00 42.75 3.41
780 1836 5.975988 TTCTGAAGGTTATAGGCTGGAAT 57.024 39.130 0.00 0.00 0.00 3.01
808 1891 2.650322 GTTGAGTTTCTGGTTCCCACA 58.350 47.619 0.00 0.00 0.00 4.17
817 1900 3.257393 CGAGATCAGGGTTGAGTTTCTG 58.743 50.000 0.00 0.00 36.61 3.02
890 1973 3.777522 AGAAATAGAAGGGTGGGTCTGAG 59.222 47.826 0.00 0.00 0.00 3.35
959 2042 4.613944 TGCAAGCAGAAATGACTCTTTTG 58.386 39.130 0.00 0.00 0.00 2.44
983 2067 3.306641 GGCCATATCTCCTCTGCTAAGTG 60.307 52.174 0.00 0.00 0.00 3.16
990 2074 1.901159 CTCTGGGCCATATCTCCTCTG 59.099 57.143 6.72 0.00 0.00 3.35
1830 3381 9.065871 GTTGCTTGATTGATGTTGAATTACTAC 57.934 33.333 0.00 0.00 0.00 2.73
1836 3387 5.803461 CGATGTTGCTTGATTGATGTTGAAT 59.197 36.000 0.00 0.00 0.00 2.57
1900 3451 3.464080 AGGGAGTAGAGCAGTGGTATACT 59.536 47.826 25.27 25.27 40.09 2.12
1901 3452 3.822167 GAGGGAGTAGAGCAGTGGTATAC 59.178 52.174 17.26 17.26 0.00 1.47
1902 3453 3.181431 GGAGGGAGTAGAGCAGTGGTATA 60.181 52.174 0.00 0.00 0.00 1.47
1903 3454 2.425102 GGAGGGAGTAGAGCAGTGGTAT 60.425 54.545 0.00 0.00 0.00 2.73
1904 3455 1.063867 GGAGGGAGTAGAGCAGTGGTA 60.064 57.143 0.00 0.00 0.00 3.25
1905 3456 0.324830 GGAGGGAGTAGAGCAGTGGT 60.325 60.000 0.00 0.00 0.00 4.16
1912 3463 2.649531 ATGAGACGGAGGGAGTAGAG 57.350 55.000 0.00 0.00 0.00 2.43
1990 3697 6.318648 TGTCTTTGTGAAACTGATGCTTACTT 59.681 34.615 0.00 0.00 38.04 2.24
1992 3699 5.909610 GTGTCTTTGTGAAACTGATGCTTAC 59.090 40.000 0.00 0.00 38.04 2.34
2039 3746 7.043325 GCTACCGTCTACATGAATTAGTTCTTG 60.043 40.741 0.00 11.00 42.26 3.02
2164 3871 6.905736 AGGAGAAGGAAGAAGAAGAAAACTT 58.094 36.000 0.00 0.00 0.00 2.66
2165 3872 6.508030 AGGAGAAGGAAGAAGAAGAAAACT 57.492 37.500 0.00 0.00 0.00 2.66
2166 3873 6.205853 GGAAGGAGAAGGAAGAAGAAGAAAAC 59.794 42.308 0.00 0.00 0.00 2.43
2169 3876 4.907875 TGGAAGGAGAAGGAAGAAGAAGAA 59.092 41.667 0.00 0.00 0.00 2.52
2171 3878 4.899352 TGGAAGGAGAAGGAAGAAGAAG 57.101 45.455 0.00 0.00 0.00 2.85
2273 3981 6.504398 ACAAGCTTCTTTTGGTTTTAGTAGC 58.496 36.000 0.00 0.00 33.93 3.58
2279 3987 6.040054 ACGGTATACAAGCTTCTTTTGGTTTT 59.960 34.615 5.01 0.00 0.00 2.43
2302 4010 9.459640 TCTATCTTTTCGATCCTGTAAATAACG 57.540 33.333 0.00 0.00 33.48 3.18
2521 4230 6.845302 TCTAAATGACACAGAATGCATGTTC 58.155 36.000 0.00 0.00 42.53 3.18
2875 4629 3.374087 GAAGAAGAAGCGGCGCTGC 62.374 63.158 37.09 34.59 39.62 5.25
2876 4630 1.294659 AAGAAGAAGAAGCGGCGCTG 61.295 55.000 37.09 13.18 39.62 5.18
2877 4631 1.004440 AAGAAGAAGAAGCGGCGCT 60.004 52.632 31.35 31.35 42.56 5.92
2878 4632 1.421877 GAAGAAGAAGAAGCGGCGC 59.578 57.895 26.86 26.86 0.00 6.53
2879 4633 1.687494 CGGAAGAAGAAGAAGCGGCG 61.687 60.000 0.51 0.51 0.00 6.46
2880 4634 1.972027 GCGGAAGAAGAAGAAGCGGC 61.972 60.000 0.00 0.00 0.00 6.53
2881 4635 0.670546 TGCGGAAGAAGAAGAAGCGG 60.671 55.000 0.00 0.00 0.00 5.52
2882 4636 0.440371 GTGCGGAAGAAGAAGAAGCG 59.560 55.000 0.00 0.00 0.00 4.68
2883 4637 1.462670 CAGTGCGGAAGAAGAAGAAGC 59.537 52.381 0.00 0.00 0.00 3.86
2884 4638 3.032017 TCAGTGCGGAAGAAGAAGAAG 57.968 47.619 0.00 0.00 0.00 2.85
2885 4639 3.131396 GTTCAGTGCGGAAGAAGAAGAA 58.869 45.455 0.00 0.00 0.00 2.52
2886 4640 2.365617 AGTTCAGTGCGGAAGAAGAAGA 59.634 45.455 0.00 0.00 0.00 2.87
2887 4641 2.734079 GAGTTCAGTGCGGAAGAAGAAG 59.266 50.000 0.00 0.00 0.00 2.85
2888 4642 2.365617 AGAGTTCAGTGCGGAAGAAGAA 59.634 45.455 0.00 0.00 0.00 2.52
2889 4643 1.964223 AGAGTTCAGTGCGGAAGAAGA 59.036 47.619 0.00 0.00 0.00 2.87
2890 4644 2.029470 AGAGAGTTCAGTGCGGAAGAAG 60.029 50.000 0.00 0.00 0.00 2.85
2891 4645 1.964223 AGAGAGTTCAGTGCGGAAGAA 59.036 47.619 0.00 0.00 0.00 2.52
2892 4646 1.542030 GAGAGAGTTCAGTGCGGAAGA 59.458 52.381 0.00 0.00 0.00 2.87
2893 4647 1.403514 GGAGAGAGTTCAGTGCGGAAG 60.404 57.143 0.00 0.00 0.00 3.46
2894 4648 0.603569 GGAGAGAGTTCAGTGCGGAA 59.396 55.000 0.00 0.00 0.00 4.30
2895 4649 0.251386 AGGAGAGAGTTCAGTGCGGA 60.251 55.000 0.00 0.00 0.00 5.54
2896 4650 0.605589 AAGGAGAGAGTTCAGTGCGG 59.394 55.000 0.00 0.00 0.00 5.69
2897 4651 2.029470 AGAAAGGAGAGAGTTCAGTGCG 60.029 50.000 0.00 0.00 0.00 5.34
2898 4652 3.676291 AGAAAGGAGAGAGTTCAGTGC 57.324 47.619 0.00 0.00 0.00 4.40
2899 4653 5.363939 ACAAAGAAAGGAGAGAGTTCAGTG 58.636 41.667 0.00 0.00 0.00 3.66
2900 4654 5.365314 AGACAAAGAAAGGAGAGAGTTCAGT 59.635 40.000 0.00 0.00 0.00 3.41
2901 4655 5.852827 AGACAAAGAAAGGAGAGAGTTCAG 58.147 41.667 0.00 0.00 0.00 3.02
2902 4656 5.878406 AGACAAAGAAAGGAGAGAGTTCA 57.122 39.130 0.00 0.00 0.00 3.18
2903 4657 6.521162 AGAAGACAAAGAAAGGAGAGAGTTC 58.479 40.000 0.00 0.00 0.00 3.01
2904 4658 6.326323 AGAGAAGACAAAGAAAGGAGAGAGTT 59.674 38.462 0.00 0.00 0.00 3.01
2905 4659 5.838521 AGAGAAGACAAAGAAAGGAGAGAGT 59.161 40.000 0.00 0.00 0.00 3.24
2906 4660 6.015519 TGAGAGAAGACAAAGAAAGGAGAGAG 60.016 42.308 0.00 0.00 0.00 3.20
2907 4661 5.835819 TGAGAGAAGACAAAGAAAGGAGAGA 59.164 40.000 0.00 0.00 0.00 3.10
2908 4662 6.095432 TGAGAGAAGACAAAGAAAGGAGAG 57.905 41.667 0.00 0.00 0.00 3.20
2909 4663 6.325028 TCTTGAGAGAAGACAAAGAAAGGAGA 59.675 38.462 0.00 0.00 0.00 3.71
2910 4664 6.520272 TCTTGAGAGAAGACAAAGAAAGGAG 58.480 40.000 0.00 0.00 0.00 3.69
2911 4665 6.485830 TCTTGAGAGAAGACAAAGAAAGGA 57.514 37.500 0.00 0.00 0.00 3.36
2912 4666 6.540189 TGTTCTTGAGAGAAGACAAAGAAAGG 59.460 38.462 0.00 0.00 42.35 3.11
2913 4667 7.545362 TGTTCTTGAGAGAAGACAAAGAAAG 57.455 36.000 0.00 0.00 42.35 2.62
2922 4676 4.081697 TGTGTGTGTGTTCTTGAGAGAAGA 60.082 41.667 0.00 0.00 42.35 2.87
2923 4677 4.033358 GTGTGTGTGTGTTCTTGAGAGAAG 59.967 45.833 0.00 0.00 42.35 2.85
2924 4678 3.932710 GTGTGTGTGTGTTCTTGAGAGAA 59.067 43.478 0.00 0.00 39.54 2.87
2925 4679 3.521560 GTGTGTGTGTGTTCTTGAGAGA 58.478 45.455 0.00 0.00 0.00 3.10
2926 4680 2.282555 CGTGTGTGTGTGTTCTTGAGAG 59.717 50.000 0.00 0.00 0.00 3.20
2927 4681 2.267426 CGTGTGTGTGTGTTCTTGAGA 58.733 47.619 0.00 0.00 0.00 3.27
2928 4682 1.267532 GCGTGTGTGTGTGTTCTTGAG 60.268 52.381 0.00 0.00 0.00 3.02
2929 4683 0.724549 GCGTGTGTGTGTGTTCTTGA 59.275 50.000 0.00 0.00 0.00 3.02
2930 4684 0.445829 TGCGTGTGTGTGTGTTCTTG 59.554 50.000 0.00 0.00 0.00 3.02
2931 4685 0.446222 GTGCGTGTGTGTGTGTTCTT 59.554 50.000 0.00 0.00 0.00 2.52
2932 4686 0.672091 TGTGCGTGTGTGTGTGTTCT 60.672 50.000 0.00 0.00 0.00 3.01
2933 4687 0.520412 GTGTGCGTGTGTGTGTGTTC 60.520 55.000 0.00 0.00 0.00 3.18
2934 4688 1.499949 GTGTGCGTGTGTGTGTGTT 59.500 52.632 0.00 0.00 0.00 3.32
2935 4689 2.735677 CGTGTGCGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
2936 4690 2.021243 CGTGTGCGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
2937 4691 3.860125 GCGTGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 40.81 3.72
3004 4758 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
3005 4759 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
3006 4760 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
3007 4761 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
3008 4762 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3009 4763 1.265635 GTTGTGTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
3010 4764 1.265365 TGTTGTGTGTGTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
3011 4765 1.265635 GTGTTGTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
3012 4766 1.265365 TGTGTTGTGTGTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
3013 4767 1.598882 TGTGTTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
3014 4768 2.161211 TCATGTGTTGTGTGTGTGTGTG 59.839 45.455 0.00 0.00 0.00 3.82
3015 4769 2.431454 TCATGTGTTGTGTGTGTGTGT 58.569 42.857 0.00 0.00 0.00 3.72
3016 4770 3.065095 TCATCATGTGTTGTGTGTGTGTG 59.935 43.478 0.00 0.00 0.00 3.82
3017 4771 3.277715 TCATCATGTGTTGTGTGTGTGT 58.722 40.909 0.00 0.00 0.00 3.72
3018 4772 3.967203 TCATCATGTGTTGTGTGTGTG 57.033 42.857 0.00 0.00 0.00 3.82
3019 4773 4.734402 GCTTTCATCATGTGTTGTGTGTGT 60.734 41.667 0.00 0.00 0.00 3.72
3020 4774 3.732219 GCTTTCATCATGTGTTGTGTGTG 59.268 43.478 0.00 0.00 0.00 3.82
3021 4775 3.243501 GGCTTTCATCATGTGTTGTGTGT 60.244 43.478 0.00 0.00 0.00 3.72
3022 4776 3.243468 TGGCTTTCATCATGTGTTGTGTG 60.243 43.478 0.00 0.00 0.00 3.82
3023 4777 2.957680 TGGCTTTCATCATGTGTTGTGT 59.042 40.909 0.00 0.00 0.00 3.72
3024 4778 3.571571 CTGGCTTTCATCATGTGTTGTG 58.428 45.455 0.00 0.00 0.00 3.33
3025 4779 2.559668 CCTGGCTTTCATCATGTGTTGT 59.440 45.455 0.00 0.00 0.00 3.32
3026 4780 2.559668 ACCTGGCTTTCATCATGTGTTG 59.440 45.455 0.00 0.00 0.00 3.33
3027 4781 2.559668 CACCTGGCTTTCATCATGTGTT 59.440 45.455 0.00 0.00 0.00 3.32
3028 4782 2.165167 CACCTGGCTTTCATCATGTGT 58.835 47.619 0.00 0.00 0.00 3.72
3029 4783 2.163010 GACACCTGGCTTTCATCATGTG 59.837 50.000 0.00 0.00 36.22 3.21
3030 4784 2.224843 TGACACCTGGCTTTCATCATGT 60.225 45.455 0.00 0.00 0.00 3.21
3031 4785 2.439409 TGACACCTGGCTTTCATCATG 58.561 47.619 0.00 0.00 0.00 3.07
3032 4786 2.885135 TGACACCTGGCTTTCATCAT 57.115 45.000 0.00 0.00 0.00 2.45
3033 4787 2.224843 ACATGACACCTGGCTTTCATCA 60.225 45.455 0.00 0.00 0.00 3.07
3034 4788 2.440409 ACATGACACCTGGCTTTCATC 58.560 47.619 0.00 0.00 0.00 2.92
3035 4789 2.592102 ACATGACACCTGGCTTTCAT 57.408 45.000 0.00 0.00 0.00 2.57
3036 4790 2.158623 AGAACATGACACCTGGCTTTCA 60.159 45.455 0.00 0.00 0.00 2.69
3037 4791 2.485814 GAGAACATGACACCTGGCTTTC 59.514 50.000 0.00 0.00 0.00 2.62
3038 4792 2.508526 GAGAACATGACACCTGGCTTT 58.491 47.619 0.00 0.00 0.00 3.51
3039 4793 1.271597 GGAGAACATGACACCTGGCTT 60.272 52.381 0.00 0.00 0.00 4.35
3040 4794 0.326264 GGAGAACATGACACCTGGCT 59.674 55.000 0.00 0.00 0.00 4.75
3041 4795 0.036732 TGGAGAACATGACACCTGGC 59.963 55.000 0.00 0.00 0.00 4.85
3042 4796 2.430465 CTTGGAGAACATGACACCTGG 58.570 52.381 0.00 0.00 0.00 4.45
3043 4797 1.808945 GCTTGGAGAACATGACACCTG 59.191 52.381 0.00 1.11 0.00 4.00
3044 4798 1.421268 TGCTTGGAGAACATGACACCT 59.579 47.619 0.00 0.00 0.00 4.00
3045 4799 1.896220 TGCTTGGAGAACATGACACC 58.104 50.000 0.00 1.96 0.00 4.16
3046 4800 3.119708 GGATTGCTTGGAGAACATGACAC 60.120 47.826 0.00 0.00 0.00 3.67
3047 4801 3.084039 GGATTGCTTGGAGAACATGACA 58.916 45.455 0.00 0.00 0.00 3.58
3048 4802 3.350833 AGGATTGCTTGGAGAACATGAC 58.649 45.455 0.00 0.00 0.00 3.06
3049 4803 3.265221 AGAGGATTGCTTGGAGAACATGA 59.735 43.478 0.00 0.00 0.00 3.07
3050 4804 3.618351 AGAGGATTGCTTGGAGAACATG 58.382 45.455 0.00 0.00 0.00 3.21
3051 4805 4.313020 AAGAGGATTGCTTGGAGAACAT 57.687 40.909 0.00 0.00 0.00 2.71
3052 4806 3.795688 AAGAGGATTGCTTGGAGAACA 57.204 42.857 0.00 0.00 0.00 3.18
3053 4807 6.375455 TCAATTAAGAGGATTGCTTGGAGAAC 59.625 38.462 0.00 0.00 35.10 3.01
3054 4808 6.484288 TCAATTAAGAGGATTGCTTGGAGAA 58.516 36.000 0.00 0.00 35.10 2.87
3055 4809 6.065976 TCAATTAAGAGGATTGCTTGGAGA 57.934 37.500 0.00 0.00 35.10 3.71
3065 4819 7.009179 TGTGAAGTCACTCAATTAAGAGGAT 57.991 36.000 12.43 0.00 46.55 3.24
3081 4835 5.086104 ACACCCTGTGTATATGTGAAGTC 57.914 43.478 0.00 0.00 45.56 3.01
3149 4946 2.579207 ACGTGGGTTGATCTACATCG 57.421 50.000 9.51 11.54 0.00 3.84
3167 4964 5.690409 TCAAAGTCAGTCGTACAGATTGAAC 59.310 40.000 12.06 8.42 45.29 3.18
3169 4966 5.220381 GTCAAAGTCAGTCGTACAGATTGA 58.780 41.667 8.18 8.18 42.30 2.57
3201 4999 2.920645 CGACGGTCTCTGCCACACT 61.921 63.158 6.57 0.00 0.00 3.55
3296 5106 1.726853 AGGCAACATCTACAGAACGC 58.273 50.000 0.00 0.00 41.41 4.84
3390 5200 1.583054 GCCGGAACATGTAGCCTAAG 58.417 55.000 5.05 5.79 0.00 2.18
3413 5223 3.540617 TGTCTTTGCAGCAAGTCTGTAA 58.459 40.909 8.12 0.00 44.00 2.41
3437 5247 1.345741 AGGCGCTCTATGCATACATGT 59.654 47.619 7.64 2.69 43.06 3.21
3510 5320 4.589908 ACTTGGTATGAAGTGATTGGGTC 58.410 43.478 0.00 0.00 34.79 4.46
3530 5340 2.149578 GAAGTTCTGTGAGCATGCACT 58.850 47.619 21.98 9.70 39.49 4.40
3584 5397 0.319813 AGGCGTGGCAAAGATTTTGC 60.320 50.000 16.05 16.05 44.22 3.68
3586 5399 4.535526 ATTTAGGCGTGGCAAAGATTTT 57.464 36.364 0.00 0.00 0.00 1.82
3700 5521 2.042537 TCCATGCCGAGCCTCTCT 60.043 61.111 0.00 0.00 0.00 3.10
3771 5592 1.841556 AAGTCGGAGTCCCTGCCAA 60.842 57.895 2.80 0.00 0.00 4.52
3772 5593 2.203788 AAGTCGGAGTCCCTGCCA 60.204 61.111 2.80 0.00 0.00 4.92
3932 5759 1.450211 CCTTCCACGACCACAACCT 59.550 57.895 0.00 0.00 0.00 3.50
3974 5801 2.768344 GAATCCCCTCGCCCCAGA 60.768 66.667 0.00 0.00 0.00 3.86
3976 5803 4.750695 TGGAATCCCCTCGCCCCA 62.751 66.667 0.00 0.00 35.38 4.96
4061 5888 4.257731 TCTACACACACACACACACAAAT 58.742 39.130 0.00 0.00 0.00 2.32
4064 5891 2.997303 GTTCTACACACACACACACACA 59.003 45.455 0.00 0.00 0.00 3.72
4065 5892 2.997303 TGTTCTACACACACACACACAC 59.003 45.455 0.00 0.00 0.00 3.82
4066 5893 3.320673 TGTTCTACACACACACACACA 57.679 42.857 0.00 0.00 0.00 3.72
4120 5967 6.127869 CCGGATTGAGAGATACGAGTCAATAT 60.128 42.308 0.00 0.00 39.25 1.28
4137 5984 2.430694 CCTGAGTGTGATACCGGATTGA 59.569 50.000 9.46 0.00 0.00 2.57
4138 5985 2.168521 ACCTGAGTGTGATACCGGATTG 59.831 50.000 9.46 0.00 0.00 2.67
4277 6128 1.839994 TGGATGAAGAAATCCTCCGCT 59.160 47.619 4.93 0.00 45.57 5.52
4335 6186 1.083806 TCGCCATTGCATCTCACGAC 61.084 55.000 0.00 0.00 37.32 4.34
4350 6201 0.802494 ATGTCGAATGGTTTGTCGCC 59.198 50.000 0.00 0.00 37.19 5.54
4437 6288 7.138081 TCATGCATGGTTATAAAATTACTGCG 58.862 34.615 25.97 0.00 0.00 5.18
4490 6341 3.508845 ATGTTGCTCCAGTAGTGGTTT 57.491 42.857 16.36 0.00 45.28 3.27
4610 6461 0.600255 CGTTCTTGCGGAGGTTGAGT 60.600 55.000 0.00 0.00 0.00 3.41
4793 6644 1.952133 CCCGTTCTTGTCGACGCAA 60.952 57.895 11.62 0.00 37.91 4.85
4811 6662 0.179097 GACAGTCGATGAAGGCCTCC 60.179 60.000 5.23 0.00 0.00 4.30
4963 6814 4.934001 CAGTAGTACGTACTCTCAGGTGAA 59.066 45.833 30.53 8.20 40.27 3.18
4970 6821 2.354199 GGCCACAGTAGTACGTACTCTC 59.646 54.545 30.53 22.91 40.27 3.20
5055 6910 6.492429 TCGCAACTCCCAACTATGTATATACT 59.508 38.462 13.89 2.84 0.00 2.12
5058 6913 5.304614 AGTCGCAACTCCCAACTATGTATAT 59.695 40.000 0.00 0.00 0.00 0.86
5066 6921 0.180406 ACAAGTCGCAACTCCCAACT 59.820 50.000 0.00 0.00 33.48 3.16
5091 6946 1.464608 AGCGATTTGACGGTCATGTTG 59.535 47.619 12.26 8.61 39.81 3.33
5215 7072 7.436673 CCATGAACAAAAATTTAGAACGAACCA 59.563 33.333 0.00 0.00 0.00 3.67
5217 7074 7.169140 AGCCATGAACAAAAATTTAGAACGAAC 59.831 33.333 0.00 0.00 0.00 3.95
5224 7081 6.647895 AGAAGCAGCCATGAACAAAAATTTAG 59.352 34.615 0.00 0.00 0.00 1.85
5226 7083 5.237779 CAGAAGCAGCCATGAACAAAAATTT 59.762 36.000 0.00 0.00 0.00 1.82
5310 7168 6.040278 TGAAGCACAAACAAATGGATAACTCA 59.960 34.615 0.00 0.00 0.00 3.41
5311 7169 6.446318 TGAAGCACAAACAAATGGATAACTC 58.554 36.000 0.00 0.00 0.00 3.01
5319 7177 3.188492 TGCACTGAAGCACAAACAAATG 58.812 40.909 0.00 0.00 40.11 2.32
5370 7229 3.072211 ACGGGCTCTTTTGCTAGTAAAC 58.928 45.455 5.40 0.00 0.00 2.01
5414 7276 6.897259 TGTTGAGTTAAGAGTGTGTGTTAC 57.103 37.500 0.00 0.00 0.00 2.50
5485 7347 2.099592 AGCGGCAACACAAATATGATGG 59.900 45.455 1.45 0.00 0.00 3.51
5694 7562 3.074412 GCTCTGAAAAATGTCGGAAGGA 58.926 45.455 0.00 0.00 32.49 3.36
5699 7567 3.374988 TGCATAGCTCTGAAAAATGTCGG 59.625 43.478 2.78 0.00 0.00 4.79
5715 7583 6.828502 ACATCAATAACTACACGTGCATAG 57.171 37.500 17.22 13.34 0.00 2.23
5783 7653 3.991051 CATACCGGCGGCGATCCT 61.991 66.667 34.49 14.05 0.00 3.24


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

AutoCloner maintained by Alex Coulton.