Multiple sequence alignment - TraesCS6D01G378100

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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 TraesCS6D01G378100 chr6D 100.000 6492 0 0 1 6492 460647318 460653809 0.000000e+00 11989.0
1 TraesCS6D01G378100 chr6D 92.737 179 12 1 6249 6427 460653472 460653649 2.320000e-64 257.0
2 TraesCS6D01G378100 chr6D 92.737 179 12 1 6155 6332 460653566 460653744 2.320000e-64 257.0
3 TraesCS6D01G378100 chr6A 94.268 4693 183 36 14 4665 606960349 606964996 0.000000e+00 7097.0
4 TraesCS6D01G378100 chr6A 85.706 1735 133 68 4680 6332 606964979 606966680 0.000000e+00 1724.0
5 TraesCS6D01G378100 chr6A 86.885 244 29 3 6249 6492 606966504 606966744 2.980000e-68 270.0
6 TraesCS6D01G378100 chr6B 95.597 2839 106 7 1 2835 701861744 701864567 0.000000e+00 4532.0
7 TraesCS6D01G378100 chr6B 93.704 1779 58 16 2910 4665 701864565 701866312 0.000000e+00 2615.0
8 TraesCS6D01G378100 chr6B 90.301 732 33 12 4680 5390 701866295 701867009 0.000000e+00 924.0
9 TraesCS6D01G378100 chr6B 88.781 722 47 15 5628 6332 701867144 701867848 0.000000e+00 854.0
10 TraesCS6D01G378100 chr6B 82.303 469 44 10 1729 2191 663798915 663798480 2.860000e-98 370.0
11 TraesCS6D01G378100 chr6B 88.797 241 23 4 6249 6489 701867673 701867909 6.370000e-75 292.0
12 TraesCS6D01G378100 chr6B 86.765 68 9 0 1640 1707 663799414 663799347 6.980000e-10 76.8
13 TraesCS6D01G378100 chr3D 74.013 304 61 14 2129 2420 609087790 609087493 2.480000e-19 108.0
14 TraesCS6D01G378100 chr3D 82.353 102 17 1 3253 3354 609086911 609086811 3.220000e-13 87.9
15 TraesCS6D01G378100 chr3D 94.872 39 2 0 6409 6447 577253196 577253158 1.950000e-05 62.1
16 TraesCS6D01G378100 chr3A 73.684 304 62 14 2129 2420 742442472 742442175 1.150000e-17 102.0
17 TraesCS6D01G378100 chr3A 86.486 74 10 0 3281 3354 742441593 742441520 1.500000e-11 82.4
18 TraesCS6D01G378100 chr5A 79.221 154 24 7 6343 6492 518406645 518406496 4.140000e-17 100.0
19 TraesCS6D01G378100 chr5A 82.105 95 9 4 2815 2908 456502219 456502306 2.510000e-09 75.0
20 TraesCS6D01G378100 chr5A 100.000 28 0 0 6246 6273 343048836 343048863 1.200000e-02 52.8
21 TraesCS6D01G378100 chr5A 100.000 28 0 0 6340 6367 343048836 343048863 1.200000e-02 52.8
22 TraesCS6D01G378100 chr3B 79.605 152 18 11 6343 6489 368916721 368916864 5.360000e-16 97.1
23 TraesCS6D01G378100 chr3B 73.267 303 65 11 2129 2420 819790846 819790549 5.360000e-16 97.1
24 TraesCS6D01G378100 chr3B 83.696 92 15 0 3263 3354 819789977 819789886 3.220000e-13 87.9
25 TraesCS6D01G378100 chr3B 90.000 40 4 0 2811 2850 423807102 423807063 1.200000e-02 52.8
26 TraesCS6D01G378100 chr2D 83.495 103 9 2 2806 2908 459300548 459300642 8.970000e-14 89.8
27 TraesCS6D01G378100 chr1D 97.778 45 1 0 2815 2859 47875638 47875682 1.940000e-10 78.7
28 TraesCS6D01G378100 chr4D 81.111 90 11 6 6409 6492 414143919 414144008 4.200000e-07 67.6
29 TraesCS6D01G378100 chr2B 85.484 62 8 1 6412 6472 47370577 47370638 5.430000e-06 63.9
30 TraesCS6D01G378100 chr4B 90.698 43 4 0 2811 2853 535219721 535219763 2.530000e-04 58.4
31 TraesCS6D01G378100 chr4B 88.889 45 4 1 2866 2910 666677118 666677075 3.000000e-03 54.7
32 TraesCS6D01G378100 chr4B 88.889 45 4 1 2866 2910 666713659 666713616 3.000000e-03 54.7
33 TraesCS6D01G378100 chr5D 100.000 28 0 0 6340 6367 258260644 258260617 1.200000e-02 52.8
34 TraesCS6D01G378100 chr5D 100.000 28 0 0 6246 6273 258260644 258260617 1.200000e-02 52.8
35 TraesCS6D01G378100 chr5B 100.000 28 0 0 6340 6367 292493395 292493368 1.200000e-02 52.8
36 TraesCS6D01G378100 chr5B 100.000 28 0 0 6246 6273 292493395 292493368 1.200000e-02 52.8
37 TraesCS6D01G378100 chr4A 94.286 35 1 1 2807 2841 29155419 29155386 1.200000e-02 52.8
38 TraesCS6D01G378100 chr4A 90.000 40 4 0 2811 2850 630844930 630844891 1.200000e-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 TraesCS6D01G378100 chr6D 460647318 460653809 6491 False 4167.666667 11989 95.158 1 6492 3 chr6D.!!$F1 6491
1 TraesCS6D01G378100 chr6A 606960349 606966744 6395 False 3030.333333 7097 88.953 14 6492 3 chr6A.!!$F1 6478
2 TraesCS6D01G378100 chr6B 701861744 701867909 6165 False 1843.400000 4532 91.436 1 6489 5 chr6B.!!$F1 6488
3 TraesCS6D01G378100 chr6B 663798480 663799414 934 True 223.400000 370 84.534 1640 2191 2 chr6B.!!$R1 551

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
557 566 0.166597 CGACTCGTAACGGCAGTGTA 59.833 55.0 0.00 0.00 0.00 2.90 F
2033 2470 0.389426 ATCCTTGTTTCCCGACGTCG 60.389 55.0 30.33 30.33 39.44 5.12 F
2720 3159 0.873054 AGATATCCGCTACACGTCGG 59.127 55.0 7.06 7.06 46.52 4.79 F
3520 4026 0.036671 TCAGTGAGCAGTCTGGCATG 60.037 55.0 1.14 0.00 35.83 4.06 F
4694 5230 0.469917 CGGGTAGCCATCACCATCTT 59.530 55.0 12.31 0.00 37.84 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2872 0.387202 CGGAGCTGTGGAGGACATAG 59.613 60.0 0.00 0.0 40.89 2.23 R
3501 4006 0.036671 CATGCCAGACTGCTCACTGA 60.037 55.0 0.00 0.0 36.38 3.41 R
4694 5230 0.322816 GGAGCAGTGCCAGGATCAAA 60.323 55.0 12.58 0.0 0.00 2.69 R
4885 5430 0.604780 CCACTTGTCCTGCTCCACAG 60.605 60.0 0.00 0.0 46.77 3.66 R
6209 6857 0.326595 TGCCAAAGATGCCTTACCGA 59.673 50.0 0.00 0.0 31.15 4.69 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
44 45 4.567159 GGGAGACTTAAAAGTAGTCATGCG 59.433 45.833 0.00 0.00 43.52 4.73
62 63 4.640789 TGCGTCCACAAGTTTTGTAATT 57.359 36.364 0.00 0.00 43.23 1.40
463 468 2.737359 GCTCCACGATACGACCAAATCA 60.737 50.000 0.00 0.00 0.00 2.57
466 471 4.613944 TCCACGATACGACCAAATCATAC 58.386 43.478 0.00 0.00 0.00 2.39
489 494 3.918258 TTTCTTCAACTTGTCACGACG 57.082 42.857 0.00 0.00 0.00 5.12
524 533 2.498481 TCACCCGATCTACGACCAAATT 59.502 45.455 0.00 0.00 45.77 1.82
557 566 0.166597 CGACTCGTAACGGCAGTGTA 59.833 55.000 0.00 0.00 0.00 2.90
571 580 2.225963 GCAGTGTATAGATACGACGCCT 59.774 50.000 0.00 0.00 36.06 5.52
583 592 3.781770 GACGCCTGATCCGCTCCAG 62.782 68.421 0.00 0.00 0.00 3.86
584 593 3.842923 CGCCTGATCCGCTCCAGT 61.843 66.667 0.00 0.00 0.00 4.00
625 634 8.623903 TGCTATTTCTCCAATTTATAGCAACAG 58.376 33.333 11.43 0.00 46.20 3.16
675 684 4.135306 CAGATACCGCCAAGTCTCTACTA 58.865 47.826 0.00 0.00 33.75 1.82
708 717 0.956633 TAACGGCAGCGGGTAGATAG 59.043 55.000 4.79 0.00 0.00 2.08
727 736 6.073981 AGATAGAGCACACAGATCTGGAATA 58.926 40.000 26.08 9.47 44.13 1.75
730 739 3.525537 AGCACACAGATCTGGAATAACG 58.474 45.455 26.08 8.57 34.19 3.18
739 748 2.437002 GGAATAACGCGGTGGGCA 60.437 61.111 7.07 0.00 43.84 5.36
789 799 3.075283 TGGATAAAAGCAGGGGAAAGTGA 59.925 43.478 0.00 0.00 0.00 3.41
916 928 3.839432 CGTTCCTCTCCTCCGCCC 61.839 72.222 0.00 0.00 0.00 6.13
1018 1030 2.355126 CAGATCGGATCGGCGTGG 60.355 66.667 12.08 0.00 0.00 4.94
1398 1413 0.830444 ACTCTGGCTCCGGTACACAA 60.830 55.000 0.00 0.00 0.00 3.33
1493 1509 5.083533 TGTTTGATGGCCAATTGTAATCC 57.916 39.130 10.96 0.93 34.23 3.01
1622 1638 2.346803 GAAAGCGACCAAGATGTAGCA 58.653 47.619 0.00 0.00 39.06 3.49
1840 2277 6.608002 ACAGTAGAGGGGTCACTAATAGAAAG 59.392 42.308 0.00 0.00 0.00 2.62
2030 2467 1.644786 GCCATCCTTGTTTCCCGACG 61.645 60.000 0.00 0.00 0.00 5.12
2033 2470 0.389426 ATCCTTGTTTCCCGACGTCG 60.389 55.000 30.33 30.33 39.44 5.12
2186 2625 1.974236 AGTAGCTCAGGAGTGCACTTT 59.026 47.619 22.65 9.99 36.73 2.66
2311 2750 1.130054 AGCACCTCAGGAAGCAAGGA 61.130 55.000 14.05 0.00 34.16 3.36
2322 2761 3.448660 AGGAAGCAAGGATGGTTATTTGC 59.551 43.478 0.09 0.09 46.70 3.68
2325 2764 3.172339 AGCAAGGATGGTTATTTGCCAA 58.828 40.909 4.60 0.00 45.22 4.52
2433 2872 8.624776 CCAATAAAGGTATTTGGAGTTGATCTC 58.375 37.037 0.00 0.00 42.07 2.75
2720 3159 0.873054 AGATATCCGCTACACGTCGG 59.127 55.000 7.06 7.06 46.52 4.79
2835 3338 4.717778 TGTACTCCCTCCGATCCAAAATAA 59.282 41.667 0.00 0.00 0.00 1.40
2836 3339 4.423625 ACTCCCTCCGATCCAAAATAAG 57.576 45.455 0.00 0.00 0.00 1.73
2837 3340 3.780850 ACTCCCTCCGATCCAAAATAAGT 59.219 43.478 0.00 0.00 0.00 2.24
2838 3341 4.227527 ACTCCCTCCGATCCAAAATAAGTT 59.772 41.667 0.00 0.00 0.00 2.66
2839 3342 5.187621 TCCCTCCGATCCAAAATAAGTTT 57.812 39.130 0.00 0.00 0.00 2.66
2840 3343 5.576128 TCCCTCCGATCCAAAATAAGTTTT 58.424 37.500 0.00 0.00 38.03 2.43
2853 3356 8.888332 CAAAATAAGTTTTGTGGTTTTGGTTC 57.112 30.769 5.67 0.00 45.76 3.62
2854 3357 8.507249 CAAAATAAGTTTTGTGGTTTTGGTTCA 58.493 29.630 5.67 0.00 45.76 3.18
2855 3358 8.622948 AAATAAGTTTTGTGGTTTTGGTTCAA 57.377 26.923 0.00 0.00 0.00 2.69
2856 3359 8.622948 AATAAGTTTTGTGGTTTTGGTTCAAA 57.377 26.923 0.00 0.00 0.00 2.69
2857 3360 8.800370 ATAAGTTTTGTGGTTTTGGTTCAAAT 57.200 26.923 0.00 0.00 33.19 2.32
2858 3361 7.517614 AAGTTTTGTGGTTTTGGTTCAAATT 57.482 28.000 0.00 0.00 33.19 1.82
2859 3362 6.907741 AGTTTTGTGGTTTTGGTTCAAATTG 58.092 32.000 0.00 0.00 33.19 2.32
2860 3363 4.954092 TTGTGGTTTTGGTTCAAATTGC 57.046 36.364 0.00 0.00 33.19 3.56
2861 3364 3.274288 TGTGGTTTTGGTTCAAATTGCC 58.726 40.909 0.00 0.00 33.19 4.52
2862 3365 3.274288 GTGGTTTTGGTTCAAATTGCCA 58.726 40.909 0.00 0.00 33.19 4.92
2863 3366 3.882288 GTGGTTTTGGTTCAAATTGCCAT 59.118 39.130 11.72 0.00 34.90 4.40
2864 3367 4.337836 GTGGTTTTGGTTCAAATTGCCATT 59.662 37.500 11.72 0.00 34.90 3.16
2865 3368 4.952335 TGGTTTTGGTTCAAATTGCCATTT 59.048 33.333 0.00 0.00 33.19 2.32
2866 3369 5.420104 TGGTTTTGGTTCAAATTGCCATTTT 59.580 32.000 0.00 0.00 33.19 1.82
2867 3370 5.747675 GGTTTTGGTTCAAATTGCCATTTTG 59.252 36.000 5.85 5.85 33.19 2.44
2868 3371 6.405176 GGTTTTGGTTCAAATTGCCATTTTGA 60.405 34.615 9.95 9.95 40.37 2.69
2869 3372 6.764308 TTTGGTTCAAATTGCCATTTTGAA 57.236 29.167 18.55 18.55 45.78 2.69
2874 3377 6.764308 TTCAAATTGCCATTTTGAACCAAA 57.236 29.167 18.55 2.55 44.12 3.28
2875 3378 6.764308 TCAAATTGCCATTTTGAACCAAAA 57.236 29.167 11.26 7.23 45.41 2.44
2876 3379 6.558909 TCAAATTGCCATTTTGAACCAAAAC 58.441 32.000 11.26 0.00 44.40 2.43
2877 3380 5.512753 AATTGCCATTTTGAACCAAAACC 57.487 34.783 6.97 1.29 44.40 3.27
2878 3381 3.634397 TGCCATTTTGAACCAAAACCA 57.366 38.095 6.97 3.45 44.40 3.67
2879 3382 3.274288 TGCCATTTTGAACCAAAACCAC 58.726 40.909 6.97 1.57 44.40 4.16
2880 3383 3.274288 GCCATTTTGAACCAAAACCACA 58.726 40.909 6.97 0.00 44.40 4.17
2881 3384 3.691609 GCCATTTTGAACCAAAACCACAA 59.308 39.130 6.97 0.00 44.40 3.33
2882 3385 4.438065 GCCATTTTGAACCAAAACCACAAC 60.438 41.667 6.97 0.00 44.40 3.32
2883 3386 4.697352 CCATTTTGAACCAAAACCACAACA 59.303 37.500 6.97 0.00 44.40 3.33
2884 3387 5.391416 CCATTTTGAACCAAAACCACAACAC 60.391 40.000 6.97 0.00 44.40 3.32
2885 3388 4.608948 TTTGAACCAAAACCACAACACT 57.391 36.364 0.00 0.00 29.89 3.55
2886 3389 4.608948 TTGAACCAAAACCACAACACTT 57.391 36.364 0.00 0.00 0.00 3.16
2887 3390 5.723672 TTGAACCAAAACCACAACACTTA 57.276 34.783 0.00 0.00 0.00 2.24
2888 3391 5.923733 TGAACCAAAACCACAACACTTAT 57.076 34.783 0.00 0.00 0.00 1.73
2889 3392 6.287589 TGAACCAAAACCACAACACTTATT 57.712 33.333 0.00 0.00 0.00 1.40
2890 3393 6.702329 TGAACCAAAACCACAACACTTATTT 58.298 32.000 0.00 0.00 0.00 1.40
2891 3394 7.162082 TGAACCAAAACCACAACACTTATTTT 58.838 30.769 0.00 0.00 0.00 1.82
2892 3395 6.976636 ACCAAAACCACAACACTTATTTTG 57.023 33.333 0.00 0.00 36.99 2.44
2893 3396 6.468543 ACCAAAACCACAACACTTATTTTGT 58.531 32.000 0.00 0.00 36.00 2.83
2894 3397 7.612677 ACCAAAACCACAACACTTATTTTGTA 58.387 30.769 0.00 0.00 36.00 2.41
2895 3398 8.261522 ACCAAAACCACAACACTTATTTTGTAT 58.738 29.630 0.00 0.00 36.00 2.29
2896 3399 8.760569 CCAAAACCACAACACTTATTTTGTATC 58.239 33.333 0.00 0.00 36.00 2.24
2897 3400 8.476142 CAAAACCACAACACTTATTTTGTATCG 58.524 33.333 0.00 0.00 34.12 2.92
2898 3401 6.249035 ACCACAACACTTATTTTGTATCGG 57.751 37.500 0.00 0.00 34.12 4.18
2899 3402 5.998981 ACCACAACACTTATTTTGTATCGGA 59.001 36.000 0.00 0.00 34.12 4.55
2900 3403 6.148811 ACCACAACACTTATTTTGTATCGGAG 59.851 38.462 0.00 0.00 34.12 4.63
2901 3404 6.403200 CCACAACACTTATTTTGTATCGGAGG 60.403 42.308 0.00 0.00 34.12 4.30
2902 3405 5.646360 ACAACACTTATTTTGTATCGGAGGG 59.354 40.000 0.00 0.00 34.12 4.30
2903 3406 5.687166 ACACTTATTTTGTATCGGAGGGA 57.313 39.130 0.00 0.00 0.00 4.20
2904 3407 5.671493 ACACTTATTTTGTATCGGAGGGAG 58.329 41.667 0.00 0.00 0.00 4.30
2905 3408 5.189145 ACACTTATTTTGTATCGGAGGGAGT 59.811 40.000 0.00 0.00 0.00 3.85
2906 3409 6.381994 ACACTTATTTTGTATCGGAGGGAGTA 59.618 38.462 0.00 0.00 0.00 2.59
2907 3410 6.924060 CACTTATTTTGTATCGGAGGGAGTAG 59.076 42.308 0.00 0.00 0.00 2.57
2908 3411 3.814005 TTTTGTATCGGAGGGAGTAGC 57.186 47.619 0.00 0.00 0.00 3.58
2909 3412 2.447408 TTGTATCGGAGGGAGTAGCA 57.553 50.000 0.00 0.00 0.00 3.49
2910 3413 2.677542 TGTATCGGAGGGAGTAGCAT 57.322 50.000 0.00 0.00 0.00 3.79
2911 3414 3.801307 TGTATCGGAGGGAGTAGCATA 57.199 47.619 0.00 0.00 0.00 3.14
2997 3500 7.255001 GTAACATTTTACACAGTTGGTACAGCT 60.255 37.037 0.00 0.00 43.14 4.24
3190 3695 6.948309 GGCTGTAATGGTAATCCTGGATATTT 59.052 38.462 10.13 0.00 34.23 1.40
3191 3696 7.451566 GGCTGTAATGGTAATCCTGGATATTTT 59.548 37.037 10.13 0.00 34.23 1.82
3195 3700 7.530426 AATGGTAATCCTGGATATTTTCTGC 57.470 36.000 10.13 0.00 34.23 4.26
3216 3721 6.478673 TCTGCAGTATTTACATACATGGAACG 59.521 38.462 14.67 0.00 38.24 3.95
3220 3725 8.342634 GCAGTATTTACATACATGGAACGATTT 58.657 33.333 0.00 0.00 38.24 2.17
3288 3793 4.092529 CCAGTCAAGTTCATCATCAAGTCG 59.907 45.833 0.00 0.00 0.00 4.18
3501 4006 7.595819 TCTCCAATAGTTGTTTGTGGAAAAT 57.404 32.000 0.00 0.00 37.90 1.82
3520 4026 0.036671 TCAGTGAGCAGTCTGGCATG 60.037 55.000 1.14 0.00 35.83 4.06
3535 4060 1.678101 GGCATGCCCTGTACAGAATTC 59.322 52.381 27.24 8.95 0.00 2.17
3540 4065 4.365514 TGCCCTGTACAGAATTCAGAAA 57.634 40.909 24.68 0.00 0.00 2.52
3541 4066 4.922206 TGCCCTGTACAGAATTCAGAAAT 58.078 39.130 24.68 0.00 0.00 2.17
3542 4067 6.061022 TGCCCTGTACAGAATTCAGAAATA 57.939 37.500 24.68 0.00 0.00 1.40
3543 4068 5.880332 TGCCCTGTACAGAATTCAGAAATAC 59.120 40.000 24.68 3.43 0.00 1.89
3544 4069 5.880332 GCCCTGTACAGAATTCAGAAATACA 59.120 40.000 24.68 7.48 0.00 2.29
3546 4071 7.254932 GCCCTGTACAGAATTCAGAAATACATC 60.255 40.741 24.68 0.00 0.00 3.06
3547 4072 7.770433 CCCTGTACAGAATTCAGAAATACATCA 59.230 37.037 24.68 0.00 0.00 3.07
3548 4073 9.334947 CCTGTACAGAATTCAGAAATACATCAT 57.665 33.333 24.68 0.00 0.00 2.45
3570 4095 7.386059 TCATTGTTTAATGTCTAGCTGACTGA 58.614 34.615 14.60 6.49 45.54 3.41
3677 4204 6.892658 AAAAATTTAGTGGCATTTTTCCCC 57.107 33.333 3.35 0.00 37.85 4.81
3740 4267 6.952773 TTTGTTGCTGTTACCTTCTTATGT 57.047 33.333 0.00 0.00 0.00 2.29
3741 4268 6.952773 TTGTTGCTGTTACCTTCTTATGTT 57.047 33.333 0.00 0.00 0.00 2.71
3742 4269 8.453238 TTTGTTGCTGTTACCTTCTTATGTTA 57.547 30.769 0.00 0.00 0.00 2.41
3797 4325 8.942338 TGTAATGGATGCTGTTACTAGTAAAG 57.058 34.615 16.82 15.75 31.37 1.85
4093 4628 9.061435 AGGTTTACTGATCAGAAAGAAGAAAAG 57.939 33.333 29.27 0.00 0.00 2.27
4122 4657 4.552355 CAAGATGCTTTGCAGATGTTTCA 58.448 39.130 0.00 0.00 43.65 2.69
4147 4682 9.582431 CAAAATATCATTTTGCTTGATCTCTGT 57.418 29.630 10.47 0.00 35.50 3.41
4524 5059 2.674852 CGTCTCATGTGACCCATCTTTG 59.325 50.000 19.41 2.41 33.70 2.77
4529 5064 4.326826 TCATGTGACCCATCTTTGTCTTC 58.673 43.478 0.00 0.00 32.67 2.87
4591 5126 2.657143 GACAACGAGGAGAGGACCTAT 58.343 52.381 0.00 0.00 40.73 2.57
4624 5159 2.163613 GGTAATCCCTTGAAAACGGCTG 59.836 50.000 0.00 0.00 0.00 4.85
4625 5160 1.995376 AATCCCTTGAAAACGGCTGT 58.005 45.000 0.00 0.00 0.00 4.40
4665 5201 2.684881 CGCTAGCCATCACCATCTTTTT 59.315 45.455 9.66 0.00 0.00 1.94
4691 5227 2.510906 GCGGGTAGCCATCACCAT 59.489 61.111 12.31 0.00 40.81 3.55
4692 5228 1.598130 GCGGGTAGCCATCACCATC 60.598 63.158 12.31 0.00 40.81 3.51
4693 5229 2.044806 GCGGGTAGCCATCACCATCT 62.045 60.000 12.31 0.00 40.81 2.90
4694 5230 0.469917 CGGGTAGCCATCACCATCTT 59.530 55.000 12.31 0.00 37.84 2.40
4695 5231 1.134098 CGGGTAGCCATCACCATCTTT 60.134 52.381 12.31 0.00 37.84 2.52
4696 5232 2.683742 CGGGTAGCCATCACCATCTTTT 60.684 50.000 12.31 0.00 37.84 2.27
4847 5392 6.864342 AGCGTGATAGTATAACACAGAAACT 58.136 36.000 0.00 0.00 43.63 2.66
4866 5411 8.436200 CAGAAACTCTGTTATCCGTTCTTAAAG 58.564 37.037 0.00 0.00 39.58 1.85
4877 5422 3.470562 CGTTCTTAAAGCTCGCTGAAAC 58.529 45.455 0.00 0.00 0.00 2.78
4885 5430 1.527311 AGCTCGCTGAAACGTCTTTTC 59.473 47.619 0.00 0.00 43.63 2.29
5068 5614 0.308376 GACTAGACTGACCGATCCGC 59.692 60.000 0.00 0.00 0.00 5.54
5115 5667 3.908213 AGAGAGAGAGAAACGAAGCAAC 58.092 45.455 0.00 0.00 0.00 4.17
5130 5682 4.308458 AACTGCGTGCGCCTGGTA 62.308 61.111 14.16 0.00 41.09 3.25
5157 5709 3.129813 TGGATGAGAGTCAAATGCAATGC 59.870 43.478 0.00 0.00 0.00 3.56
5158 5710 3.129813 GGATGAGAGTCAAATGCAATGCA 59.870 43.478 11.44 11.44 44.86 3.96
5159 5711 4.381185 GGATGAGAGTCAAATGCAATGCAA 60.381 41.667 13.45 0.00 43.62 4.08
5160 5712 4.794278 TGAGAGTCAAATGCAATGCAAT 57.206 36.364 13.45 0.00 43.62 3.56
5161 5713 4.490743 TGAGAGTCAAATGCAATGCAATG 58.509 39.130 13.45 14.67 43.62 2.82
5178 5730 3.122278 GCAATGTCAATGACAATGTGTGC 59.878 43.478 26.30 21.28 45.96 4.57
5436 5997 5.587844 GCCAGATATGTGATGTCTGTTTCTT 59.412 40.000 0.46 0.00 44.20 2.52
5437 5998 6.238320 GCCAGATATGTGATGTCTGTTTCTTC 60.238 42.308 0.46 0.00 44.20 2.87
5454 6015 4.537135 TCTTCTATCTTGTGTGTGGGTC 57.463 45.455 0.00 0.00 0.00 4.46
5456 6017 4.220821 TCTTCTATCTTGTGTGTGGGTCTC 59.779 45.833 0.00 0.00 0.00 3.36
5473 6034 2.043992 TCTCGGGTGTCTTTGAAAGGA 58.956 47.619 4.94 0.00 0.00 3.36
5478 6039 3.084786 GGGTGTCTTTGAAAGGAGATGG 58.915 50.000 4.94 0.00 0.00 3.51
5482 6043 4.397417 GTGTCTTTGAAAGGAGATGGATGG 59.603 45.833 4.94 0.00 0.00 3.51
5483 6044 4.289410 TGTCTTTGAAAGGAGATGGATGGA 59.711 41.667 4.94 0.00 0.00 3.41
5484 6045 5.044624 TGTCTTTGAAAGGAGATGGATGGAT 60.045 40.000 4.94 0.00 0.00 3.41
5485 6046 5.298777 GTCTTTGAAAGGAGATGGATGGATG 59.701 44.000 4.94 0.00 0.00 3.51
5486 6047 4.868172 TTGAAAGGAGATGGATGGATGT 57.132 40.909 0.00 0.00 0.00 3.06
5495 6056 5.195940 GAGATGGATGGATGTTTTCCTTGA 58.804 41.667 0.00 0.00 45.68 3.02
5532 6093 3.558608 TTTCCTTTGTTGGGATGGGAT 57.441 42.857 0.00 0.00 32.41 3.85
5533 6094 2.530460 TCCTTTGTTGGGATGGGATG 57.470 50.000 0.00 0.00 0.00 3.51
5539 6100 3.334604 TGGGATGGGATGCCACTC 58.665 61.111 8.67 7.60 46.53 3.51
5577 6138 6.258727 GTGGTGTGGTGAAGAATATGATGTAG 59.741 42.308 0.00 0.00 0.00 2.74
5578 6139 5.237344 GGTGTGGTGAAGAATATGATGTAGC 59.763 44.000 0.00 0.00 0.00 3.58
5580 6141 6.484643 GTGTGGTGAAGAATATGATGTAGCAT 59.515 38.462 0.00 0.00 0.00 3.79
5582 6143 6.148480 GTGGTGAAGAATATGATGTAGCATCC 59.852 42.308 6.65 0.00 0.00 3.51
5609 6196 6.103997 GGAGCATTTTGTTTCATGATGATGT 58.896 36.000 0.00 0.00 0.00 3.06
5610 6197 6.255020 GGAGCATTTTGTTTCATGATGATGTC 59.745 38.462 0.00 0.00 0.00 3.06
5611 6198 6.931838 AGCATTTTGTTTCATGATGATGTCT 58.068 32.000 0.00 0.00 0.00 3.41
5612 6199 8.058667 AGCATTTTGTTTCATGATGATGTCTA 57.941 30.769 0.00 0.00 0.00 2.59
5613 6200 7.972277 AGCATTTTGTTTCATGATGATGTCTAC 59.028 33.333 0.00 0.00 0.00 2.59
5615 6202 5.469373 TTGTTTCATGATGATGTCTACGC 57.531 39.130 0.00 0.00 0.00 4.42
5616 6203 4.758688 TGTTTCATGATGATGTCTACGCT 58.241 39.130 0.00 0.00 0.00 5.07
5617 6204 4.567959 TGTTTCATGATGATGTCTACGCTG 59.432 41.667 0.00 0.00 0.00 5.18
5618 6205 4.391405 TTCATGATGATGTCTACGCTGT 57.609 40.909 0.00 0.00 0.00 4.40
5619 6206 5.514274 TTCATGATGATGTCTACGCTGTA 57.486 39.130 0.00 0.00 0.00 2.74
5620 6207 5.113502 TCATGATGATGTCTACGCTGTAG 57.886 43.478 8.77 8.77 0.00 2.74
5621 6208 4.580580 TCATGATGATGTCTACGCTGTAGT 59.419 41.667 13.06 0.00 0.00 2.73
5622 6209 4.553756 TGATGATGTCTACGCTGTAGTC 57.446 45.455 13.06 9.56 0.00 2.59
5623 6210 4.200092 TGATGATGTCTACGCTGTAGTCT 58.800 43.478 13.06 3.01 0.00 3.24
5624 6211 4.035675 TGATGATGTCTACGCTGTAGTCTG 59.964 45.833 13.06 0.00 0.00 3.51
5626 6213 0.809385 TGTCTACGCTGTAGTCTGCC 59.191 55.000 13.06 2.61 35.56 4.85
5631 6218 2.580867 GCTGTAGTCTGCCGCTCG 60.581 66.667 0.00 0.00 33.40 5.03
5706 6307 5.515270 CGGTGTTGGTATGATATATGTAGCG 59.485 44.000 0.00 0.00 0.00 4.26
5754 6364 9.969001 ACATTACCATTATGATGATGATGATGA 57.031 29.630 3.84 0.00 35.16 2.92
5759 6369 9.125026 ACCATTATGATGATGATGATGATGATG 57.875 33.333 0.00 0.00 35.16 3.07
5760 6370 9.342308 CCATTATGATGATGATGATGATGATGA 57.658 33.333 0.00 0.00 35.16 2.92
5838 6448 1.000896 AATTGGGGAAGGCGTCAGG 60.001 57.895 2.23 0.00 0.00 3.86
5891 6501 2.289882 CCATGTGGATACGGATCAGCAT 60.290 50.000 10.45 9.90 42.51 3.79
5892 6502 2.531522 TGTGGATACGGATCAGCATG 57.468 50.000 10.45 0.00 42.51 4.06
5893 6503 1.762370 TGTGGATACGGATCAGCATGT 59.238 47.619 10.45 0.00 42.51 3.21
5928 6542 4.158764 AGACGAAGAAATGGTCTCCTACTG 59.841 45.833 0.00 0.00 42.77 2.74
6034 6676 8.936864 AGAATGTAAGGTTTCATCTTTCGTTAG 58.063 33.333 0.00 0.00 0.00 2.34
6056 6703 0.984230 TCACACCACCTCTTCATCCC 59.016 55.000 0.00 0.00 0.00 3.85
6076 6724 1.003718 CCTCCCACCTTTCACCGAC 60.004 63.158 0.00 0.00 0.00 4.79
6101 6749 1.265905 CTCGGTTTTTGACCCCTTTCG 59.734 52.381 0.00 0.00 46.35 3.46
6212 6860 8.671384 TTTCCTATGATAAAACTTGGTATCGG 57.329 34.615 0.00 0.00 30.64 4.18
6213 6861 7.369551 TCCTATGATAAAACTTGGTATCGGT 57.630 36.000 0.00 0.00 30.64 4.69
6214 6862 8.481492 TCCTATGATAAAACTTGGTATCGGTA 57.519 34.615 0.00 0.00 30.64 4.02
6215 6863 8.926374 TCCTATGATAAAACTTGGTATCGGTAA 58.074 33.333 0.00 0.00 30.64 2.85
6216 6864 9.204570 CCTATGATAAAACTTGGTATCGGTAAG 57.795 37.037 0.00 0.00 30.64 2.34
6217 6865 9.204570 CTATGATAAAACTTGGTATCGGTAAGG 57.795 37.037 0.00 0.00 30.64 2.69
6218 6866 5.818857 TGATAAAACTTGGTATCGGTAAGGC 59.181 40.000 0.00 0.00 30.64 4.35
6219 6867 3.706600 AAACTTGGTATCGGTAAGGCA 57.293 42.857 0.00 0.00 0.00 4.75
6220 6868 3.926058 AACTTGGTATCGGTAAGGCAT 57.074 42.857 0.00 0.00 0.00 4.40
6221 6869 3.470645 ACTTGGTATCGGTAAGGCATC 57.529 47.619 0.00 0.00 0.00 3.91
6222 6870 3.039011 ACTTGGTATCGGTAAGGCATCT 58.961 45.455 0.00 0.00 0.00 2.90
6223 6871 3.454812 ACTTGGTATCGGTAAGGCATCTT 59.545 43.478 0.00 0.00 37.03 2.40
6224 6872 4.080526 ACTTGGTATCGGTAAGGCATCTTT 60.081 41.667 0.00 0.00 34.59 2.52
6225 6873 3.804036 TGGTATCGGTAAGGCATCTTTG 58.196 45.455 0.00 0.00 34.59 2.77
6226 6874 3.139077 GGTATCGGTAAGGCATCTTTGG 58.861 50.000 0.00 0.00 34.59 3.28
6409 7057 6.834168 AAAAATTTGGTACCGATCAGACAT 57.166 33.333 7.57 0.00 0.00 3.06
6414 7062 4.123497 TGGTACCGATCAGACATCTTTG 57.877 45.455 7.57 0.00 0.00 2.77
6415 7063 3.118775 TGGTACCGATCAGACATCTTTGG 60.119 47.826 7.57 0.00 0.00 3.28
6458 7107 3.913548 TTCATGGTCCGTGAACAAATG 57.086 42.857 20.63 0.00 34.89 2.32
6461 7110 4.078537 TCATGGTCCGTGAACAAATGAAT 58.921 39.130 11.60 0.00 31.09 2.57
6464 7113 5.811399 TGGTCCGTGAACAAATGAATATC 57.189 39.130 0.00 0.00 0.00 1.63
6465 7114 5.249420 TGGTCCGTGAACAAATGAATATCA 58.751 37.500 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.562108 AAGTCTCCCTTTGTCCCTCTA 57.438 47.619 0.00 0.00 0.00 2.43
62 63 8.504005 GCTTCTTTACACTAGAGCATTTTACAA 58.496 33.333 0.00 0.00 0.00 2.41
403 404 4.574828 GCTAACAAAGACAACTGTGAAGGA 59.425 41.667 0.00 0.00 35.12 3.36
463 468 7.061905 CGTCGTGACAAGTTGAAGAAATAGTAT 59.938 37.037 10.54 0.00 0.00 2.12
466 471 5.388475 CCGTCGTGACAAGTTGAAGAAATAG 60.388 44.000 10.54 0.00 0.00 1.73
483 488 4.264614 GTGATTTATCTACACACCGTCGTG 59.735 45.833 0.00 0.25 46.11 4.35
489 494 4.395959 TCGGGTGATTTATCTACACACC 57.604 45.455 0.00 0.00 46.79 4.16
524 533 3.724374 ACGAGTCGGAGAAACAATGAAA 58.276 40.909 18.30 0.00 39.69 2.69
557 566 1.738350 CGGATCAGGCGTCGTATCTAT 59.262 52.381 0.00 0.00 0.00 1.98
571 580 2.265589 TCGTATACTGGAGCGGATCA 57.734 50.000 0.56 0.00 0.00 2.92
583 592 9.284594 GAGAAATAGCAGAGATTGATCGTATAC 57.715 37.037 0.00 0.00 0.00 1.47
584 593 8.462811 GGAGAAATAGCAGAGATTGATCGTATA 58.537 37.037 0.00 0.00 0.00 1.47
625 634 2.283298 TCGGGTCGTGTATCTAGACAC 58.717 52.381 0.00 0.00 45.19 3.67
675 684 4.616953 CTGCCGTTACAATTTGGAAAAGT 58.383 39.130 0.00 0.00 0.00 2.66
708 717 3.553511 CGTTATTCCAGATCTGTGTGCTC 59.446 47.826 21.11 6.96 0.00 4.26
789 799 4.538891 ACCCTTGTAGTAAAACCCTAGCAT 59.461 41.667 0.00 0.00 0.00 3.79
1398 1413 4.273318 AGAGCCTGTCACAAAAGAAAAGT 58.727 39.130 0.00 0.00 0.00 2.66
1441 1456 7.293018 CAAAATGCATTTCCAAGAAAGCTTAC 58.707 34.615 24.28 0.00 31.81 2.34
1622 1638 4.582869 TGTCTGAATTATGACTTGCTGCT 58.417 39.130 0.00 0.00 34.57 4.24
1840 2277 0.392461 TAAGTTGTCCGCATCTGCCC 60.392 55.000 0.00 0.00 37.91 5.36
2030 2467 1.862827 ACTTGTTTAACGTCTGCCGAC 59.137 47.619 0.00 0.00 40.70 4.79
2033 2470 1.332375 TGCACTTGTTTAACGTCTGCC 59.668 47.619 0.00 0.00 0.00 4.85
2186 2625 4.438255 CCATTGTCATGGCCACCA 57.562 55.556 8.16 1.65 43.95 4.17
2209 2648 1.002544 CCGGATAGAATGGAGAAGCCC 59.997 57.143 0.00 0.00 34.97 5.19
2311 2750 7.038373 AGTCACCTTTATTTGGCAAATAACCAT 60.038 33.333 33.70 22.57 41.61 3.55
2322 2761 7.308589 CCTTGTTCTACAGTCACCTTTATTTGG 60.309 40.741 0.00 0.00 0.00 3.28
2325 2764 7.016268 TCTCCTTGTTCTACAGTCACCTTTATT 59.984 37.037 0.00 0.00 0.00 1.40
2433 2872 0.387202 CGGAGCTGTGGAGGACATAG 59.613 60.000 0.00 0.00 40.89 2.23
2562 3001 0.036010 ATTTCCTCCACAGCTCCACG 60.036 55.000 0.00 0.00 0.00 4.94
2720 3159 3.869272 CGTTGCATCTGCGCCCTC 61.869 66.667 4.18 0.00 45.83 4.30
2835 3338 6.569418 GCAATTTGAACCAAAACCACAAAACT 60.569 34.615 0.00 0.00 36.90 2.66
2836 3339 5.570973 GCAATTTGAACCAAAACCACAAAAC 59.429 36.000 0.00 0.00 36.90 2.43
2837 3340 5.335976 GGCAATTTGAACCAAAACCACAAAA 60.336 36.000 0.00 0.00 36.90 2.44
2838 3341 4.156739 GGCAATTTGAACCAAAACCACAAA 59.843 37.500 0.00 0.00 36.90 2.83
2839 3342 3.691609 GGCAATTTGAACCAAAACCACAA 59.308 39.130 0.00 0.00 36.90 3.33
2840 3343 3.274288 GGCAATTTGAACCAAAACCACA 58.726 40.909 0.00 0.00 36.90 4.17
2841 3344 3.274288 TGGCAATTTGAACCAAAACCAC 58.726 40.909 0.00 0.00 36.90 4.16
2842 3345 3.634397 TGGCAATTTGAACCAAAACCA 57.366 38.095 0.00 0.00 36.90 3.67
2843 3346 5.512753 AAATGGCAATTTGAACCAAAACC 57.487 34.783 0.00 0.00 36.90 3.27
2844 3347 6.558909 TCAAAATGGCAATTTGAACCAAAAC 58.441 32.000 24.37 0.00 42.19 2.43
2845 3348 6.764308 TCAAAATGGCAATTTGAACCAAAA 57.236 29.167 24.37 4.10 42.19 2.44
2846 3349 6.764308 TTCAAAATGGCAATTTGAACCAAA 57.236 29.167 29.95 14.86 46.34 3.28
2852 3355 6.405176 GGTTTTGGTTCAAAATGGCAATTTGA 60.405 34.615 23.16 23.16 43.66 2.69
2853 3356 5.747675 GGTTTTGGTTCAAAATGGCAATTTG 59.252 36.000 19.53 19.53 43.66 2.32
2854 3357 5.420104 TGGTTTTGGTTCAAAATGGCAATTT 59.580 32.000 8.72 0.00 43.66 1.82
2855 3358 4.952335 TGGTTTTGGTTCAAAATGGCAATT 59.048 33.333 8.72 0.00 43.66 2.32
2856 3359 4.337836 GTGGTTTTGGTTCAAAATGGCAAT 59.662 37.500 8.72 0.00 43.66 3.56
2857 3360 3.691609 GTGGTTTTGGTTCAAAATGGCAA 59.308 39.130 8.72 0.00 43.66 4.52
2858 3361 3.274288 GTGGTTTTGGTTCAAAATGGCA 58.726 40.909 8.72 0.00 43.66 4.92
2859 3362 3.274288 TGTGGTTTTGGTTCAAAATGGC 58.726 40.909 8.72 3.99 43.66 4.40
2860 3363 4.697352 TGTTGTGGTTTTGGTTCAAAATGG 59.303 37.500 8.72 0.00 43.66 3.16
2861 3364 5.411053 AGTGTTGTGGTTTTGGTTCAAAATG 59.589 36.000 8.72 0.00 43.66 2.32
2862 3365 5.555966 AGTGTTGTGGTTTTGGTTCAAAAT 58.444 33.333 8.72 0.00 43.66 1.82
2863 3366 4.962155 AGTGTTGTGGTTTTGGTTCAAAA 58.038 34.783 2.14 2.14 40.41 2.44
2864 3367 4.608948 AGTGTTGTGGTTTTGGTTCAAA 57.391 36.364 0.00 0.00 0.00 2.69
2865 3368 4.608948 AAGTGTTGTGGTTTTGGTTCAA 57.391 36.364 0.00 0.00 0.00 2.69
2866 3369 5.923733 ATAAGTGTTGTGGTTTTGGTTCA 57.076 34.783 0.00 0.00 0.00 3.18
2867 3370 7.118535 ACAAAATAAGTGTTGTGGTTTTGGTTC 59.881 33.333 11.54 0.00 39.54 3.62
2868 3371 6.937465 ACAAAATAAGTGTTGTGGTTTTGGTT 59.063 30.769 11.54 0.00 39.54 3.67
2869 3372 6.468543 ACAAAATAAGTGTTGTGGTTTTGGT 58.531 32.000 11.54 0.00 39.54 3.67
2870 3373 6.976636 ACAAAATAAGTGTTGTGGTTTTGG 57.023 33.333 11.54 0.00 39.54 3.28
2871 3374 8.476142 CGATACAAAATAAGTGTTGTGGTTTTG 58.524 33.333 0.00 0.00 38.40 2.44
2872 3375 7.650104 CCGATACAAAATAAGTGTTGTGGTTTT 59.350 33.333 0.00 0.00 38.40 2.43
2873 3376 7.013464 TCCGATACAAAATAAGTGTTGTGGTTT 59.987 33.333 0.00 0.00 38.40 3.27
2874 3377 6.487331 TCCGATACAAAATAAGTGTTGTGGTT 59.513 34.615 0.00 0.00 38.40 3.67
2875 3378 5.998981 TCCGATACAAAATAAGTGTTGTGGT 59.001 36.000 0.00 0.00 38.40 4.16
2876 3379 6.403200 CCTCCGATACAAAATAAGTGTTGTGG 60.403 42.308 0.00 0.00 38.40 4.17
2877 3380 6.403200 CCCTCCGATACAAAATAAGTGTTGTG 60.403 42.308 0.00 0.00 38.40 3.33
2878 3381 5.646360 CCCTCCGATACAAAATAAGTGTTGT 59.354 40.000 0.00 0.00 40.88 3.32
2879 3382 5.878116 TCCCTCCGATACAAAATAAGTGTTG 59.122 40.000 0.00 0.00 0.00 3.33
2880 3383 6.057321 TCCCTCCGATACAAAATAAGTGTT 57.943 37.500 0.00 0.00 0.00 3.32
2881 3384 5.189145 ACTCCCTCCGATACAAAATAAGTGT 59.811 40.000 0.00 0.00 0.00 3.55
2882 3385 5.671493 ACTCCCTCCGATACAAAATAAGTG 58.329 41.667 0.00 0.00 0.00 3.16
2883 3386 5.952347 ACTCCCTCCGATACAAAATAAGT 57.048 39.130 0.00 0.00 0.00 2.24
2884 3387 5.927115 GCTACTCCCTCCGATACAAAATAAG 59.073 44.000 0.00 0.00 0.00 1.73
2885 3388 5.364446 TGCTACTCCCTCCGATACAAAATAA 59.636 40.000 0.00 0.00 0.00 1.40
2886 3389 4.897076 TGCTACTCCCTCCGATACAAAATA 59.103 41.667 0.00 0.00 0.00 1.40
2887 3390 3.709653 TGCTACTCCCTCCGATACAAAAT 59.290 43.478 0.00 0.00 0.00 1.82
2888 3391 3.101437 TGCTACTCCCTCCGATACAAAA 58.899 45.455 0.00 0.00 0.00 2.44
2889 3392 2.742348 TGCTACTCCCTCCGATACAAA 58.258 47.619 0.00 0.00 0.00 2.83
2890 3393 2.447408 TGCTACTCCCTCCGATACAA 57.553 50.000 0.00 0.00 0.00 2.41
2891 3394 2.677542 ATGCTACTCCCTCCGATACA 57.322 50.000 0.00 0.00 0.00 2.29
2892 3395 3.688235 AGTATGCTACTCCCTCCGATAC 58.312 50.000 0.00 0.00 32.47 2.24
2893 3396 4.079970 CAAGTATGCTACTCCCTCCGATA 58.920 47.826 0.00 0.00 38.26 2.92
2894 3397 2.894126 CAAGTATGCTACTCCCTCCGAT 59.106 50.000 0.00 0.00 38.26 4.18
2895 3398 2.307768 CAAGTATGCTACTCCCTCCGA 58.692 52.381 0.00 0.00 38.26 4.55
2896 3399 2.032620 ACAAGTATGCTACTCCCTCCG 58.967 52.381 0.00 0.00 38.26 4.63
2897 3400 5.542779 CAATACAAGTATGCTACTCCCTCC 58.457 45.833 0.00 0.00 38.26 4.30
2898 3401 4.991687 GCAATACAAGTATGCTACTCCCTC 59.008 45.833 0.00 0.00 38.26 4.30
2899 3402 4.202367 GGCAATACAAGTATGCTACTCCCT 60.202 45.833 11.54 0.00 38.26 4.20
2900 3403 4.065789 GGCAATACAAGTATGCTACTCCC 58.934 47.826 11.54 0.00 38.26 4.30
2901 3404 4.703897 TGGCAATACAAGTATGCTACTCC 58.296 43.478 11.54 0.00 38.26 3.85
2902 3405 6.867662 AATGGCAATACAAGTATGCTACTC 57.132 37.500 0.00 1.36 38.26 2.59
2903 3406 7.483307 CAAAATGGCAATACAAGTATGCTACT 58.517 34.615 0.00 0.00 41.73 2.57
2904 3407 6.198966 GCAAAATGGCAATACAAGTATGCTAC 59.801 38.462 0.00 0.00 0.00 3.58
2905 3408 6.272318 GCAAAATGGCAATACAAGTATGCTA 58.728 36.000 0.00 8.07 0.00 3.49
2906 3409 5.111293 GCAAAATGGCAATACAAGTATGCT 58.889 37.500 0.00 0.00 0.00 3.79
2907 3410 4.270808 GGCAAAATGGCAATACAAGTATGC 59.729 41.667 0.00 0.84 43.14 3.14
2908 3411 5.521010 CAGGCAAAATGGCAATACAAGTATG 59.479 40.000 6.68 0.00 46.46 2.39
2909 3412 5.395546 CCAGGCAAAATGGCAATACAAGTAT 60.396 40.000 6.68 0.00 46.46 2.12
2910 3413 4.081752 CCAGGCAAAATGGCAATACAAGTA 60.082 41.667 6.68 0.00 46.46 2.24
2911 3414 3.306919 CCAGGCAAAATGGCAATACAAGT 60.307 43.478 6.68 0.00 46.46 3.16
3190 3695 7.011016 CGTTCCATGTATGTAAATACTGCAGAA 59.989 37.037 23.35 0.00 0.00 3.02
3191 3696 6.478673 CGTTCCATGTATGTAAATACTGCAGA 59.521 38.462 23.35 4.31 0.00 4.26
3195 3700 9.864034 GAAATCGTTCCATGTATGTAAATACTG 57.136 33.333 4.68 1.22 0.00 2.74
3288 3793 6.690194 ATTGATAGCTCAGGAATGTTGAAC 57.310 37.500 0.00 0.00 31.68 3.18
3386 3891 9.326413 AGTGTATGGTTGCTAATAAGTCAATAC 57.674 33.333 0.00 0.00 0.00 1.89
3501 4006 0.036671 CATGCCAGACTGCTCACTGA 60.037 55.000 0.00 0.00 36.38 3.41
3520 4026 5.880332 TGTATTTCTGAATTCTGTACAGGGC 59.120 40.000 22.48 10.01 33.19 5.19
3540 4065 9.836864 TCAGCTAGACATTAAACAATGATGTAT 57.163 29.630 4.46 0.00 39.40 2.29
3541 4066 9.098355 GTCAGCTAGACATTAAACAATGATGTA 57.902 33.333 10.30 0.00 46.77 2.29
3542 4067 7.978982 GTCAGCTAGACATTAAACAATGATGT 58.021 34.615 10.30 0.00 46.77 3.06
3608 4135 5.899299 ACTGCTAAAATGCATCATCCTTTC 58.101 37.500 0.00 0.00 42.48 2.62
3675 4202 7.573096 GCAATTATGGTAATACATCAAGACGGG 60.573 40.741 0.00 0.00 32.39 5.28
3676 4203 7.173218 AGCAATTATGGTAATACATCAAGACGG 59.827 37.037 0.00 0.00 34.98 4.79
3677 4204 8.087982 AGCAATTATGGTAATACATCAAGACG 57.912 34.615 0.00 0.00 34.98 4.18
3742 4269 9.090692 CTCTGAAGACAAAATTGAAACATGTTT 57.909 29.630 23.49 23.49 35.14 2.83
3797 4325 0.536006 ACACTGAGGCTGCCTTCAAC 60.536 55.000 24.26 10.51 31.76 3.18
3956 4484 3.640967 GAGTCCATCTCTTCAGGTGCTAT 59.359 47.826 0.00 0.00 39.86 2.97
4147 4682 8.055181 AGGAAATCCTTAGATGAGCATAAACAA 58.945 33.333 0.00 0.00 46.09 2.83
4266 4801 1.332997 GATCGCTTGGCAGATTTCTGG 59.667 52.381 9.49 0.00 43.94 3.86
4331 4866 1.179174 GCCTTGACCTGGGAACAACC 61.179 60.000 0.00 0.00 42.06 3.77
4624 5159 2.544267 CGACTCTGAGGTTTTTCCACAC 59.456 50.000 9.85 0.00 39.02 3.82
4625 5160 2.833794 CGACTCTGAGGTTTTTCCACA 58.166 47.619 9.85 0.00 39.02 4.17
4669 5205 0.885196 GTGATGGCTACCCGCAAAAA 59.115 50.000 0.00 0.00 41.67 1.94
4670 5206 0.963355 GGTGATGGCTACCCGCAAAA 60.963 55.000 0.00 0.00 41.67 2.44
4671 5207 1.377987 GGTGATGGCTACCCGCAAA 60.378 57.895 0.00 0.00 41.67 3.68
4672 5208 1.920734 ATGGTGATGGCTACCCGCAA 61.921 55.000 0.00 0.00 41.67 4.85
4673 5209 2.324014 GATGGTGATGGCTACCCGCA 62.324 60.000 0.00 0.00 41.67 5.69
4674 5210 1.598130 GATGGTGATGGCTACCCGC 60.598 63.158 0.00 0.00 37.40 6.13
4675 5211 0.469917 AAGATGGTGATGGCTACCCG 59.530 55.000 0.00 0.00 37.40 5.28
4676 5212 2.689983 CAAAAGATGGTGATGGCTACCC 59.310 50.000 0.00 0.00 37.40 3.69
4677 5213 3.620488 TCAAAAGATGGTGATGGCTACC 58.380 45.455 0.00 0.00 38.71 3.18
4678 5214 4.276926 GGATCAAAAGATGGTGATGGCTAC 59.723 45.833 0.00 0.00 34.61 3.58
4679 5215 4.166725 AGGATCAAAAGATGGTGATGGCTA 59.833 41.667 0.00 0.00 34.61 3.93
4680 5216 3.053095 AGGATCAAAAGATGGTGATGGCT 60.053 43.478 0.00 0.00 34.61 4.75
4681 5217 3.067742 CAGGATCAAAAGATGGTGATGGC 59.932 47.826 0.00 0.00 34.61 4.40
4682 5218 3.635373 CCAGGATCAAAAGATGGTGATGG 59.365 47.826 0.00 0.00 34.61 3.51
4683 5219 3.067742 GCCAGGATCAAAAGATGGTGATG 59.932 47.826 0.00 0.00 34.61 3.07
4684 5220 3.294214 GCCAGGATCAAAAGATGGTGAT 58.706 45.455 0.00 0.00 37.19 3.06
4685 5221 2.041485 TGCCAGGATCAAAAGATGGTGA 59.959 45.455 0.00 0.00 33.42 4.02
4686 5222 2.165030 GTGCCAGGATCAAAAGATGGTG 59.835 50.000 0.00 0.00 33.42 4.17
4687 5223 2.042162 AGTGCCAGGATCAAAAGATGGT 59.958 45.455 0.00 0.00 33.42 3.55
4688 5224 2.426024 CAGTGCCAGGATCAAAAGATGG 59.574 50.000 0.00 0.00 0.00 3.51
4689 5225 2.159282 GCAGTGCCAGGATCAAAAGATG 60.159 50.000 2.85 0.00 0.00 2.90
4690 5226 2.097825 GCAGTGCCAGGATCAAAAGAT 58.902 47.619 2.85 0.00 0.00 2.40
4691 5227 1.074405 AGCAGTGCCAGGATCAAAAGA 59.926 47.619 12.58 0.00 0.00 2.52
4692 5228 1.471684 GAGCAGTGCCAGGATCAAAAG 59.528 52.381 12.58 0.00 0.00 2.27
4693 5229 1.538047 GAGCAGTGCCAGGATCAAAA 58.462 50.000 12.58 0.00 0.00 2.44
4694 5230 0.322816 GGAGCAGTGCCAGGATCAAA 60.323 55.000 12.58 0.00 0.00 2.69
4695 5231 1.300963 GGAGCAGTGCCAGGATCAA 59.699 57.895 12.58 0.00 0.00 2.57
4696 5232 1.276859 ATGGAGCAGTGCCAGGATCA 61.277 55.000 12.58 1.92 39.11 2.92
4847 5392 5.100259 CGAGCTTTAAGAACGGATAACAGA 58.900 41.667 0.00 0.00 0.00 3.41
4855 5400 1.710013 TCAGCGAGCTTTAAGAACGG 58.290 50.000 0.00 0.00 0.00 4.44
4860 5405 2.731976 AGACGTTTCAGCGAGCTTTAAG 59.268 45.455 0.00 0.00 35.59 1.85
4866 5411 1.527311 AGAAAAGACGTTTCAGCGAGC 59.473 47.619 14.92 0.00 46.98 5.03
4885 5430 0.604780 CCACTTGTCCTGCTCCACAG 60.605 60.000 0.00 0.00 46.77 3.66
5099 5651 1.136502 CGCAGTTGCTTCGTTTCTCTC 60.137 52.381 2.29 0.00 39.32 3.20
5115 5667 2.819595 AATACCAGGCGCACGCAG 60.820 61.111 17.69 8.47 44.11 5.18
5130 5682 3.380637 GCATTTGACTCTCATCCAGCAAT 59.619 43.478 0.00 0.00 0.00 3.56
5157 5709 4.149221 GTGCACACATTGTCATTGACATTG 59.851 41.667 27.72 27.72 44.43 2.82
5158 5710 4.300803 GTGCACACATTGTCATTGACATT 58.699 39.130 19.63 13.52 42.40 2.71
5159 5711 3.305539 GGTGCACACATTGTCATTGACAT 60.306 43.478 19.63 7.90 42.40 3.06
5160 5712 2.034432 GGTGCACACATTGTCATTGACA 59.966 45.455 20.43 15.41 41.09 3.58
5161 5713 2.294233 AGGTGCACACATTGTCATTGAC 59.706 45.455 20.43 9.93 0.00 3.18
5308 5865 7.490657 TTTCTAGTTACATACACCCACAGAT 57.509 36.000 0.00 0.00 0.00 2.90
5410 5971 5.876651 AACAGACATCACATATCTGGCTA 57.123 39.130 5.54 0.00 43.46 3.93
5436 5997 2.492088 CGAGACCCACACACAAGATAGA 59.508 50.000 0.00 0.00 0.00 1.98
5437 5998 2.417379 CCGAGACCCACACACAAGATAG 60.417 54.545 0.00 0.00 0.00 2.08
5454 6015 2.037251 TCTCCTTTCAAAGACACCCGAG 59.963 50.000 0.00 0.00 0.00 4.63
5456 6017 2.543777 TCTCCTTTCAAAGACACCCG 57.456 50.000 0.00 0.00 0.00 5.28
5482 6043 4.952335 ACAGATCCCATCAAGGAAAACATC 59.048 41.667 0.00 0.00 40.04 3.06
5483 6044 4.939255 ACAGATCCCATCAAGGAAAACAT 58.061 39.130 0.00 0.00 40.04 2.71
5484 6045 4.387026 ACAGATCCCATCAAGGAAAACA 57.613 40.909 0.00 0.00 40.04 2.83
5485 6046 4.524328 ACAACAGATCCCATCAAGGAAAAC 59.476 41.667 0.00 0.00 40.04 2.43
5486 6047 4.523943 CACAACAGATCCCATCAAGGAAAA 59.476 41.667 0.00 0.00 40.04 2.29
5495 6056 2.762327 GGAAATGCACAACAGATCCCAT 59.238 45.455 0.00 0.00 33.03 4.00
5532 6093 1.134753 CTGCAAACAAACAGAGTGGCA 59.865 47.619 0.00 0.00 35.90 4.92
5533 6094 1.134946 ACTGCAAACAAACAGAGTGGC 59.865 47.619 0.00 0.00 37.35 5.01
5537 6098 2.164219 ACACCACTGCAAACAAACAGAG 59.836 45.455 0.00 0.00 37.35 3.35
5539 6100 2.261345 CACACCACTGCAAACAAACAG 58.739 47.619 0.00 0.00 39.86 3.16
5577 6138 2.973694 ACAAAATGCTCCATGGATGC 57.026 45.000 16.63 20.16 0.00 3.91
5578 6139 4.823157 TGAAACAAAATGCTCCATGGATG 58.177 39.130 16.63 12.10 0.00 3.51
5580 6141 4.527427 TCATGAAACAAAATGCTCCATGGA 59.473 37.500 15.27 15.27 0.00 3.41
5582 6143 6.103330 TCATCATGAAACAAAATGCTCCATG 58.897 36.000 0.00 0.00 0.00 3.66
5609 6196 1.989966 GCGGCAGACTACAGCGTAGA 61.990 60.000 18.36 0.00 0.00 2.59
5610 6197 1.586564 GCGGCAGACTACAGCGTAG 60.587 63.158 12.26 12.26 0.00 3.51
5611 6198 1.989966 GAGCGGCAGACTACAGCGTA 61.990 60.000 1.45 0.00 0.00 4.42
5612 6199 3.343788 GAGCGGCAGACTACAGCGT 62.344 63.158 1.45 0.00 0.00 5.07
5613 6200 2.580867 GAGCGGCAGACTACAGCG 60.581 66.667 1.45 0.00 0.00 5.18
5615 6202 2.103143 CCGAGCGGCAGACTACAG 59.897 66.667 1.45 0.00 0.00 2.74
5616 6203 3.449227 CCCGAGCGGCAGACTACA 61.449 66.667 1.45 0.00 0.00 2.74
5617 6204 2.221906 TTTCCCGAGCGGCAGACTAC 62.222 60.000 1.45 0.00 0.00 2.73
5618 6205 1.327690 ATTTCCCGAGCGGCAGACTA 61.328 55.000 1.45 0.00 0.00 2.59
5619 6206 1.327690 TATTTCCCGAGCGGCAGACT 61.328 55.000 1.45 0.00 0.00 3.24
5620 6207 0.876342 CTATTTCCCGAGCGGCAGAC 60.876 60.000 1.45 0.00 0.00 3.51
5621 6208 1.441729 CTATTTCCCGAGCGGCAGA 59.558 57.895 1.45 0.00 0.00 4.26
5622 6209 1.595382 CCTATTTCCCGAGCGGCAG 60.595 63.158 1.45 0.00 0.00 4.85
5623 6210 1.906105 AACCTATTTCCCGAGCGGCA 61.906 55.000 1.45 0.00 0.00 5.69
5624 6211 1.153229 AACCTATTTCCCGAGCGGC 60.153 57.895 2.79 0.00 0.00 6.53
5626 6213 0.462047 AGCAACCTATTTCCCGAGCG 60.462 55.000 0.00 0.00 0.00 5.03
5631 6218 2.100197 GGACCAAGCAACCTATTTCCC 58.900 52.381 0.00 0.00 0.00 3.97
5675 6264 2.577700 TCATACCAACACCGCAAAAGT 58.422 42.857 0.00 0.00 0.00 2.66
5680 6278 5.222079 ACATATATCATACCAACACCGCA 57.778 39.130 0.00 0.00 0.00 5.69
5706 6307 7.320443 TGTTCTCATACATTGCCATTTCTAC 57.680 36.000 0.00 0.00 0.00 2.59
5787 6397 3.560989 AGCTCTATCTGCTGGCCC 58.439 61.111 0.00 0.00 39.56 5.80
5838 6448 4.008933 ACCAGTCAGGCGTCAGGC 62.009 66.667 0.00 0.00 43.14 4.85
5891 6501 2.759839 TCGTCTGGATATACCCCACA 57.240 50.000 0.00 0.00 38.00 4.17
5892 6502 3.228453 TCTTCGTCTGGATATACCCCAC 58.772 50.000 0.00 0.00 38.00 4.61
5893 6503 3.605726 TCTTCGTCTGGATATACCCCA 57.394 47.619 0.00 0.00 38.00 4.96
5934 6548 7.015292 AGAGATAGAGAAAACCACGGCATAATA 59.985 37.037 0.00 0.00 0.00 0.98
5935 6549 5.930135 AGATAGAGAAAACCACGGCATAAT 58.070 37.500 0.00 0.00 0.00 1.28
5940 6554 3.528597 AGAGATAGAGAAAACCACGGC 57.471 47.619 0.00 0.00 0.00 5.68
6012 6654 6.228258 AGCTAACGAAAGATGAAACCTTACA 58.772 36.000 0.00 0.00 0.00 2.41
6029 6671 1.000955 AGAGGTGGTGTGAAGCTAACG 59.999 52.381 0.00 0.00 0.00 3.18
6034 6676 2.079925 GATGAAGAGGTGGTGTGAAGC 58.920 52.381 0.00 0.00 0.00 3.86
6056 6703 1.192146 TCGGTGAAAGGTGGGAGGAG 61.192 60.000 0.00 0.00 0.00 3.69
6101 6749 4.082026 CCAAAGATTGGTCTGATGAAACCC 60.082 45.833 0.87 0.00 45.93 4.11
6126 6774 9.472361 CCAAACATTGATCTGATTTATTGGATC 57.528 33.333 10.44 0.00 36.55 3.36
6128 6776 8.365060 ACCAAACATTGATCTGATTTATTGGA 57.635 30.769 17.49 0.00 37.58 3.53
6201 6849 3.039011 AGATGCCTTACCGATACCAAGT 58.961 45.455 0.00 0.00 0.00 3.16
6204 6852 3.433031 CCAAAGATGCCTTACCGATACCA 60.433 47.826 0.00 0.00 31.15 3.25
6205 6853 3.139077 CCAAAGATGCCTTACCGATACC 58.861 50.000 0.00 0.00 31.15 2.73
6206 6854 2.548480 GCCAAAGATGCCTTACCGATAC 59.452 50.000 0.00 0.00 31.15 2.24
6207 6855 2.171659 TGCCAAAGATGCCTTACCGATA 59.828 45.455 0.00 0.00 31.15 2.92
6208 6856 1.064758 TGCCAAAGATGCCTTACCGAT 60.065 47.619 0.00 0.00 31.15 4.18
6209 6857 0.326595 TGCCAAAGATGCCTTACCGA 59.673 50.000 0.00 0.00 31.15 4.69
6210 6858 1.135402 GTTGCCAAAGATGCCTTACCG 60.135 52.381 0.00 0.00 31.15 4.02
6211 6859 1.204704 GGTTGCCAAAGATGCCTTACC 59.795 52.381 0.00 0.00 31.15 2.85
6212 6860 1.204704 GGGTTGCCAAAGATGCCTTAC 59.795 52.381 0.00 0.00 31.15 2.34
6213 6861 1.203112 TGGGTTGCCAAAGATGCCTTA 60.203 47.619 0.00 0.00 31.15 2.69
6214 6862 0.471591 TGGGTTGCCAAAGATGCCTT 60.472 50.000 0.00 0.00 0.00 4.35
6215 6863 0.471591 TTGGGTTGCCAAAGATGCCT 60.472 50.000 0.00 0.00 0.00 4.75
6216 6864 0.614812 ATTGGGTTGCCAAAGATGCC 59.385 50.000 0.00 0.00 33.20 4.40
6217 6865 3.608316 TTATTGGGTTGCCAAAGATGC 57.392 42.857 0.00 0.00 33.20 3.91
6280 6928 8.846211 CCGGTACCAAGTTTTATCATATGAAAT 58.154 33.333 13.54 0.00 0.00 2.17
6281 6929 7.830201 ACCGGTACCAAGTTTTATCATATGAAA 59.170 33.333 4.49 3.10 0.00 2.69
6282 6930 7.340256 ACCGGTACCAAGTTTTATCATATGAA 58.660 34.615 4.49 0.00 0.00 2.57
6283 6931 6.891388 ACCGGTACCAAGTTTTATCATATGA 58.109 36.000 4.49 8.10 0.00 2.15
6284 6932 8.665643 TTACCGGTACCAAGTTTTATCATATG 57.334 34.615 15.53 0.00 0.00 1.78
6285 6933 7.935210 CCTTACCGGTACCAAGTTTTATCATAT 59.065 37.037 15.53 0.00 0.00 1.78
6286 6934 7.274447 CCTTACCGGTACCAAGTTTTATCATA 58.726 38.462 15.53 0.00 0.00 2.15
6287 6935 6.117488 CCTTACCGGTACCAAGTTTTATCAT 58.883 40.000 15.53 0.00 0.00 2.45
6288 6936 5.490159 CCTTACCGGTACCAAGTTTTATCA 58.510 41.667 15.53 0.00 0.00 2.15
6289 6937 4.333649 GCCTTACCGGTACCAAGTTTTATC 59.666 45.833 15.53 0.00 34.25 1.75
6290 6938 4.263418 TGCCTTACCGGTACCAAGTTTTAT 60.263 41.667 15.53 0.00 34.25 1.40
6291 6939 3.072184 TGCCTTACCGGTACCAAGTTTTA 59.928 43.478 15.53 0.00 34.25 1.52
6292 6940 2.158638 TGCCTTACCGGTACCAAGTTTT 60.159 45.455 15.53 0.00 34.25 2.43
6293 6941 1.420891 TGCCTTACCGGTACCAAGTTT 59.579 47.619 15.53 0.00 34.25 2.66
6294 6942 1.058284 TGCCTTACCGGTACCAAGTT 58.942 50.000 15.53 0.00 34.25 2.66
6295 6943 1.208776 GATGCCTTACCGGTACCAAGT 59.791 52.381 15.53 11.19 34.25 3.16
6296 6944 1.485066 AGATGCCTTACCGGTACCAAG 59.515 52.381 15.53 11.38 34.25 3.61
6297 6945 1.575419 AGATGCCTTACCGGTACCAA 58.425 50.000 15.53 0.00 34.25 3.67
6298 6946 1.575419 AAGATGCCTTACCGGTACCA 58.425 50.000 15.53 12.29 34.25 3.25
6311 6959 3.608316 TTATTGGGTTGCCAAAGATGC 57.392 42.857 0.00 0.00 33.20 3.91
6379 7027 8.287439 TGATCGGTACCAAATTTTTATCACAT 57.713 30.769 13.54 0.00 0.00 3.21
6381 7029 7.908601 GTCTGATCGGTACCAAATTTTTATCAC 59.091 37.037 13.54 0.00 0.00 3.06
6386 7034 6.659242 AGATGTCTGATCGGTACCAAATTTTT 59.341 34.615 13.54 0.00 0.00 1.94
6391 7039 4.819105 AAGATGTCTGATCGGTACCAAA 57.181 40.909 13.54 0.00 0.00 3.28
6442 7091 5.249420 TGATATTCATTTGTTCACGGACCA 58.751 37.500 0.00 0.00 0.00 4.02
6443 7092 5.811399 TGATATTCATTTGTTCACGGACC 57.189 39.130 0.00 0.00 0.00 4.46
6446 7095 8.347771 AGATTGATGATATTCATTTGTTCACGG 58.652 33.333 0.00 0.00 37.20 4.94
6447 7096 9.726232 AAGATTGATGATATTCATTTGTTCACG 57.274 29.630 0.00 0.00 37.20 4.35


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

AutoCloner maintained by Alex Coulton.