Multiple sequence alignment - TraesCS2A01G262700

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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 TraesCS2A01G262700 chr2A 100.000 6511 0 0 1 6511 414988701 414995211 0.000000e+00 12024.0
1 TraesCS2A01G262700 chr2B 95.196 3601 118 21 2932 6511 385566255 385562689 0.000000e+00 5640.0
2 TraesCS2A01G262700 chr2B 96.130 1111 31 3 553 1652 385568712 385567603 0.000000e+00 1803.0
3 TraesCS2A01G262700 chr2B 96.367 578 17 2 2197 2773 385566828 385566254 0.000000e+00 948.0
4 TraesCS2A01G262700 chr2B 96.203 553 17 3 1648 2198 385567492 385566942 0.000000e+00 902.0
5 TraesCS2A01G262700 chr2B 90.441 408 12 4 21 406 385569500 385569098 4.500000e-141 512.0
6 TraesCS2A01G262700 chr2D 96.029 2191 66 9 601 2773 317948176 317945989 0.000000e+00 3544.0
7 TraesCS2A01G262700 chr2D 97.991 1543 25 3 3588 5127 317945734 317944195 0.000000e+00 2673.0
8 TraesCS2A01G262700 chr2D 94.088 1404 50 14 5123 6511 317944094 317942709 0.000000e+00 2102.0
9 TraesCS2A01G262700 chr2D 97.266 256 7 0 2932 3187 317945990 317945735 1.000000e-117 435.0
10 TraesCS2A01G262700 chr2D 80.167 479 47 27 5 447 317948636 317948170 1.360000e-81 315.0
11 TraesCS2A01G262700 chr2D 94.048 168 10 0 2767 2934 305514864 305515031 8.380000e-64 255.0
12 TraesCS2A01G262700 chr2D 90.000 190 17 2 2745 2933 521564004 521564192 1.810000e-60 244.0
13 TraesCS2A01G262700 chr6A 86.059 954 103 21 980 1914 71537034 71537976 0.000000e+00 998.0
14 TraesCS2A01G262700 chr6A 85.688 552 67 9 3674 4220 71539277 71539821 7.320000e-159 571.0
15 TraesCS2A01G262700 chr6A 80.282 568 86 20 2064 2625 71538189 71538736 7.860000e-109 405.0
16 TraesCS2A01G262700 chr6A 91.061 179 13 2 444 622 151467131 151466956 8.440000e-59 239.0
17 TraesCS2A01G262700 chr6A 90.058 171 14 3 5202 5371 71541228 71541396 1.100000e-52 219.0
18 TraesCS2A01G262700 chr6A 77.020 396 60 22 4668 5046 71540601 71540982 1.430000e-46 198.0
19 TraesCS2A01G262700 chr6A 98.039 51 1 0 5635 5685 414871220 414871270 8.990000e-14 89.8
20 TraesCS2A01G262700 chr6A 93.103 58 3 1 5633 5689 76743623 76743680 4.180000e-12 84.2
21 TraesCS2A01G262700 chr6A 100.000 30 0 0 6143 6172 497474154 497474183 1.000000e-03 56.5
22 TraesCS2A01G262700 chr6A 94.286 35 2 0 6315 6349 617102615 617102581 3.000000e-03 54.7
23 TraesCS2A01G262700 chr6B 84.360 1055 123 23 888 1914 127604381 127605421 0.000000e+00 996.0
24 TraesCS2A01G262700 chr6B 86.029 544 61 11 3674 4206 127606883 127607422 2.630000e-158 569.0
25 TraesCS2A01G262700 chr6B 84.211 380 48 8 2249 2625 127605976 127606346 6.210000e-95 359.0
26 TraesCS2A01G262700 chr6B 91.949 236 17 2 4228 4462 127607602 127607836 4.870000e-86 329.0
27 TraesCS2A01G262700 chr6B 92.179 179 11 2 444 622 226361518 226361693 3.900000e-62 250.0
28 TraesCS2A01G262700 chr6B 91.329 173 11 4 444 614 172738532 172738362 3.930000e-57 233.0
29 TraesCS2A01G262700 chr6B 80.368 326 43 14 5202 5506 127608985 127609310 1.830000e-55 228.0
30 TraesCS2A01G262700 chr6D 84.104 1038 132 18 888 1906 56909019 56910042 0.000000e+00 972.0
31 TraesCS2A01G262700 chr6D 85.075 536 70 6 3674 4206 56911578 56912106 7.430000e-149 538.0
32 TraesCS2A01G262700 chr6D 84.348 230 28 6 5142 5370 56913453 56913675 1.100000e-52 219.0
33 TraesCS2A01G262700 chr6D 77.834 397 56 23 4668 5046 56912879 56913261 3.950000e-52 217.0
34 TraesCS2A01G262700 chr6D 94.545 55 2 1 5630 5684 419440829 419440882 4.180000e-12 84.2
35 TraesCS2A01G262700 chr6D 91.379 58 4 1 5633 5689 60240664 60240721 1.950000e-10 78.7
36 TraesCS2A01G262700 chr4B 95.679 162 7 0 2772 2933 483266540 483266379 1.800000e-65 261.0
37 TraesCS2A01G262700 chr4B 91.860 172 12 2 442 612 406389294 406389464 8.440000e-59 239.0
38 TraesCS2A01G262700 chr5B 95.062 162 8 0 2772 2933 539322883 539322722 8.380000e-64 255.0
39 TraesCS2A01G262700 chr5B 94.545 55 3 0 5631 5685 211004093 211004039 1.160000e-12 86.1
40 TraesCS2A01G262700 chr3D 94.545 165 9 0 2769 2933 238999411 238999575 8.380000e-64 255.0
41 TraesCS2A01G262700 chr3D 91.160 181 10 6 444 623 87926161 87925986 2.350000e-59 241.0
42 TraesCS2A01G262700 chr3D 97.674 43 0 1 5626 5667 19787997 19788039 9.060000e-09 73.1
43 TraesCS2A01G262700 chr4D 93.976 166 10 0 2769 2934 230542547 230542712 1.080000e-62 252.0
44 TraesCS2A01G262700 chr4D 94.643 56 3 0 5630 5685 363960572 363960517 3.230000e-13 87.9
45 TraesCS2A01G262700 chrUn 93.023 172 10 2 2763 2934 100779955 100780124 3.900000e-62 250.0
46 TraesCS2A01G262700 chrUn 96.154 52 2 0 5633 5684 321532968 321532917 1.160000e-12 86.1
47 TraesCS2A01G262700 chr1A 92.442 172 11 2 2763 2933 15540167 15539997 1.810000e-60 244.0
48 TraesCS2A01G262700 chr1A 98.182 55 1 0 5629 5683 120017863 120017809 5.370000e-16 97.1
49 TraesCS2A01G262700 chr1A 96.364 55 2 0 5630 5684 377940074 377940020 2.500000e-14 91.6
50 TraesCS2A01G262700 chr1A 94.643 56 3 0 5629 5684 516825563 516825618 3.230000e-13 87.9
51 TraesCS2A01G262700 chr5A 93.252 163 11 0 444 606 426896902 426896740 2.350000e-59 241.0
52 TraesCS2A01G262700 chr4A 92.814 167 11 1 444 609 137966979 137967145 2.350000e-59 241.0
53 TraesCS2A01G262700 chr4A 92.353 170 12 1 444 612 137972830 137972661 2.350000e-59 241.0
54 TraesCS2A01G262700 chr7D 91.813 171 14 0 444 614 454079408 454079238 8.440000e-59 239.0
55 TraesCS2A01G262700 chr7D 86.154 65 2 6 2737 2799 593550357 593550298 5.450000e-06 63.9
56 TraesCS2A01G262700 chr5D 88.060 201 20 4 2735 2934 296949323 296949520 1.090000e-57 235.0
57 TraesCS2A01G262700 chr5D 98.148 54 1 0 5631 5684 22835690 22835637 1.930000e-15 95.3
58 TraesCS2A01G262700 chr5D 91.071 56 5 0 5629 5684 29506393 29506448 7.000000e-10 76.8
59 TraesCS2A01G262700 chr3B 98.113 53 1 0 5631 5683 61984846 61984794 6.950000e-15 93.5
60 TraesCS2A01G262700 chr3B 94.828 58 3 0 5628 5685 1596414 1596357 2.500000e-14 91.6
61 TraesCS2A01G262700 chr3B 90.141 71 5 1 5616 5684 796850077 796850147 2.500000e-14 91.6
62 TraesCS2A01G262700 chr7B 96.364 55 2 0 5630 5684 688926976 688926922 2.500000e-14 91.6
63 TraesCS2A01G262700 chr7B 96.296 54 2 0 5631 5684 728507274 728507221 8.990000e-14 89.8
64 TraesCS2A01G262700 chr1D 96.296 54 2 0 5632 5685 491604738 491604791 8.990000e-14 89.8


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 TraesCS2A01G262700 chr2A 414988701 414995211 6510 False 12024.0 12024 100.00000 1 6511 1 chr2A.!!$F1 6510
1 TraesCS2A01G262700 chr2B 385562689 385569500 6811 True 1961.0 5640 94.86740 21 6511 5 chr2B.!!$R1 6490
2 TraesCS2A01G262700 chr2D 317942709 317948636 5927 True 1813.8 3544 93.10820 5 6511 5 chr2D.!!$R1 6506
3 TraesCS2A01G262700 chr6A 71537034 71541396 4362 False 478.2 998 83.82140 980 5371 5 chr6A.!!$F4 4391
4 TraesCS2A01G262700 chr6B 127604381 127609310 4929 False 496.2 996 85.38340 888 5506 5 chr6B.!!$F2 4618
5 TraesCS2A01G262700 chr6D 56909019 56913675 4656 False 486.5 972 82.84025 888 5370 4 chr6D.!!$F3 4482

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
216 261 0.108424 CACTGCCTCTCCTTTCTCCG 60.108 60.000 0.00 0.00 0.00 4.63 F
1128 1496 0.891373 TGGAGAGTGTGCAGACTAGC 59.109 55.000 17.62 11.41 0.00 3.42 F
2420 3338 1.340017 TGGTGCTGAGATACAAAGGGC 60.340 52.381 0.00 0.00 0.00 5.19 F
3200 4172 0.039617 TTGTATTGTGCAACGCTGGC 60.040 50.000 0.00 0.00 42.39 4.85 F
3341 4313 0.240411 GTTGCTGAGGCTTTGCTGAG 59.760 55.000 12.54 0.00 39.59 3.35 F
3500 4472 1.136529 CAGCGTTCAGATGTGTGTTCG 60.137 52.381 0.00 0.00 0.00 3.95 F
5275 7285 1.471119 AAGTACTCGCCGAGAATCCA 58.529 50.000 22.80 0.00 33.32 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2772 2.286067 GCACATTGTCTAGCGATGCTTC 60.286 50.000 11.93 0.0 41.64 3.86 R
2918 3867 1.213926 TCTACCTACTCCCTCCGTTCC 59.786 57.143 0.00 0.0 0.00 3.62 R
3423 4395 1.032014 ACACAACATGTCCAAGGCAC 58.968 50.000 0.00 0.0 36.54 5.01 R
5140 7150 4.080695 AGGCACTGAAATCTCATCTGCTAA 60.081 41.667 0.32 0.0 37.18 3.09 R
5275 7285 2.744202 CCGATACTGCTCAAGTTGCTTT 59.256 45.455 0.00 0.0 40.56 3.51 R
5340 7350 7.341256 ACACAGCTCCAGATTCAAAAATATCAT 59.659 33.333 0.00 0.0 0.00 2.45 R
6383 8439 1.224592 GGATTCGGTGCCTGGTCAT 59.775 57.895 0.00 0.0 0.00 3.06 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 2.173569 GACAGGGATTAATGGCCTCAGT 59.826 50.000 3.32 0.00 0.00 3.41
64 65 2.015456 TTCTCTCTCACTGGGCTGAA 57.985 50.000 0.00 0.00 0.00 3.02
106 107 3.457380 CAGGGAGAGAGAAATGAATGGGA 59.543 47.826 0.00 0.00 0.00 4.37
216 261 0.108424 CACTGCCTCTCCTTTCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
221 266 1.562783 CCTCTCCTTTCTCCGTTCCT 58.437 55.000 0.00 0.00 0.00 3.36
406 472 4.022416 TCGGTTACTGGCGTAGTTTTCTAA 60.022 41.667 0.00 0.00 40.89 2.10
407 473 4.325472 CGGTTACTGGCGTAGTTTTCTAAG 59.675 45.833 0.00 0.00 40.89 2.18
408 474 5.233225 GGTTACTGGCGTAGTTTTCTAAGT 58.767 41.667 0.00 0.00 40.89 2.24
409 475 6.389906 GGTTACTGGCGTAGTTTTCTAAGTA 58.610 40.000 0.00 0.00 40.89 2.24
415 481 7.117379 ACTGGCGTAGTTTTCTAAGTATTCAAC 59.883 37.037 0.00 0.00 35.67 3.18
440 506 5.614923 ACTCCGTAATAGATCATCTCGTG 57.385 43.478 0.00 0.00 0.00 4.35
441 507 5.306394 ACTCCGTAATAGATCATCTCGTGA 58.694 41.667 0.00 0.00 42.06 4.35
442 508 5.410132 ACTCCGTAATAGATCATCTCGTGAG 59.590 44.000 0.00 1.13 40.92 3.51
443 509 5.306394 TCCGTAATAGATCATCTCGTGAGT 58.694 41.667 0.00 0.00 40.92 3.41
444 510 6.461640 TCCGTAATAGATCATCTCGTGAGTA 58.538 40.000 0.00 0.00 40.92 2.59
447 513 7.095144 CCGTAATAGATCATCTCGTGAGTACTT 60.095 40.741 0.00 0.00 40.92 2.24
452 518 4.223556 TCATCTCGTGAGTACTTCCTCT 57.776 45.455 0.00 0.00 32.50 3.69
546 839 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
547 840 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
548 841 7.615403 AGTGTAGATTCACTCATTTTGCTCTA 58.385 34.615 0.00 0.00 44.07 2.43
577 921 9.878667 TGTAGTCCGTATTGAAATATCTGAAAA 57.121 29.630 0.00 0.00 0.00 2.29
583 927 9.922305 CCGTATTGAAATATCTGAAAAGACTTC 57.078 33.333 0.00 0.00 0.00 3.01
595 939 8.758633 TCTGAAAAGACTTCTATTTAGGAACG 57.241 34.615 0.00 0.00 0.00 3.95
597 941 7.673180 TGAAAAGACTTCTATTTAGGAACGGA 58.327 34.615 0.00 0.00 0.00 4.69
677 1021 3.631686 TCTGACTTCATGGTGGTTTTGTG 59.368 43.478 0.00 0.00 0.00 3.33
836 1183 6.496911 TGAGAGGATTGGACCGATTTATCATA 59.503 38.462 0.00 0.00 34.73 2.15
862 1209 3.409026 AGCCACCTAAACTCAGTGAAG 57.591 47.619 0.00 0.00 33.21 3.02
892 1239 5.106987 GCCTGCTAAATTGTGAATTGGTTTG 60.107 40.000 0.00 0.00 0.00 2.93
1128 1496 0.891373 TGGAGAGTGTGCAGACTAGC 59.109 55.000 17.62 11.41 0.00 3.42
1494 1862 3.820467 AGTTTGACATTCCGATTGCTGAA 59.180 39.130 0.00 0.00 0.00 3.02
2021 2568 5.463286 CAGCTTAATTGCACTTGATGTCAA 58.537 37.500 0.00 0.00 34.99 3.18
2089 2723 8.853077 TTCTCAAATCTGATACAAGAACATGT 57.147 30.769 0.00 0.00 37.32 3.21
2137 2772 5.414144 TGTCATTACATGTGTGGTTATGTGG 59.586 40.000 9.11 0.00 37.98 4.17
2290 3207 8.094798 TGGTAGCTACAACTTTAAAGTCATTG 57.905 34.615 24.75 17.10 38.57 2.82
2420 3338 1.340017 TGGTGCTGAGATACAAAGGGC 60.340 52.381 0.00 0.00 0.00 5.19
2518 3436 4.889409 GGCCTATTGGACAATCAGAATTCA 59.111 41.667 8.44 0.00 42.34 2.57
2627 3545 7.267857 TCAGTGTTATGATCTGATGATTCGTT 58.732 34.615 0.00 0.00 34.00 3.85
2628 3546 7.223387 TCAGTGTTATGATCTGATGATTCGTTG 59.777 37.037 0.00 0.00 34.00 4.10
2776 3725 7.969536 ACTGACATTGCATGTTATATACTCC 57.030 36.000 0.00 0.00 45.03 3.85
2777 3726 6.936900 ACTGACATTGCATGTTATATACTCCC 59.063 38.462 0.00 0.00 45.03 4.30
2778 3727 7.078249 TGACATTGCATGTTATATACTCCCT 57.922 36.000 0.00 0.00 45.03 4.20
2779 3728 7.161404 TGACATTGCATGTTATATACTCCCTC 58.839 38.462 0.00 0.00 45.03 4.30
2780 3729 6.476378 ACATTGCATGTTATATACTCCCTCC 58.524 40.000 0.00 0.00 41.63 4.30
2781 3730 4.801330 TGCATGTTATATACTCCCTCCG 57.199 45.455 0.00 0.00 0.00 4.63
2782 3731 4.157246 TGCATGTTATATACTCCCTCCGT 58.843 43.478 0.00 0.00 0.00 4.69
2783 3732 4.591498 TGCATGTTATATACTCCCTCCGTT 59.409 41.667 0.00 0.00 0.00 4.44
2784 3733 5.169295 GCATGTTATATACTCCCTCCGTTC 58.831 45.833 0.00 0.00 0.00 3.95
2785 3734 5.721232 CATGTTATATACTCCCTCCGTTCC 58.279 45.833 0.00 0.00 0.00 3.62
2786 3735 5.070823 TGTTATATACTCCCTCCGTTCCT 57.929 43.478 0.00 0.00 0.00 3.36
2787 3736 6.204852 TGTTATATACTCCCTCCGTTCCTA 57.795 41.667 0.00 0.00 0.00 2.94
2788 3737 6.613699 TGTTATATACTCCCTCCGTTCCTAA 58.386 40.000 0.00 0.00 0.00 2.69
2789 3738 7.068702 TGTTATATACTCCCTCCGTTCCTAAA 58.931 38.462 0.00 0.00 0.00 1.85
2790 3739 7.731688 TGTTATATACTCCCTCCGTTCCTAAAT 59.268 37.037 0.00 0.00 0.00 1.40
2791 3740 9.247861 GTTATATACTCCCTCCGTTCCTAAATA 57.752 37.037 0.00 0.00 0.00 1.40
2795 3744 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2796 3745 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2797 3746 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2798 3747 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2799 3748 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2800 3749 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2801 3750 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2802 3751 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2820 3769 9.606631 AGTCTTTGTAGAGATTTCATTATGGAC 57.393 33.333 0.00 0.00 0.00 4.02
2821 3770 8.831550 GTCTTTGTAGAGATTTCATTATGGACC 58.168 37.037 0.00 0.00 0.00 4.46
2822 3771 8.548025 TCTTTGTAGAGATTTCATTATGGACCA 58.452 33.333 0.00 0.00 0.00 4.02
2823 3772 8.506168 TTTGTAGAGATTTCATTATGGACCAC 57.494 34.615 0.00 0.00 0.00 4.16
2824 3773 7.194112 TGTAGAGATTTCATTATGGACCACA 57.806 36.000 0.00 0.00 0.00 4.17
2825 3774 7.805163 TGTAGAGATTTCATTATGGACCACAT 58.195 34.615 0.00 0.00 43.68 3.21
2826 3775 8.933653 TGTAGAGATTTCATTATGGACCACATA 58.066 33.333 0.00 0.00 41.03 2.29
2827 3776 9.209175 GTAGAGATTTCATTATGGACCACATAC 57.791 37.037 0.00 0.00 41.61 2.39
2828 3777 6.931281 AGAGATTTCATTATGGACCACATACG 59.069 38.462 0.00 0.00 41.61 3.06
2829 3778 5.997746 AGATTTCATTATGGACCACATACGG 59.002 40.000 0.00 0.00 41.61 4.02
2830 3779 5.360649 TTTCATTATGGACCACATACGGA 57.639 39.130 0.00 0.00 41.61 4.69
2831 3780 5.560722 TTCATTATGGACCACATACGGAT 57.439 39.130 0.00 0.00 41.61 4.18
2832 3781 4.893608 TCATTATGGACCACATACGGATG 58.106 43.478 5.94 5.94 41.61 3.51
2833 3782 4.591072 TCATTATGGACCACATACGGATGA 59.409 41.667 16.36 0.00 41.61 2.92
2834 3783 5.071115 TCATTATGGACCACATACGGATGAA 59.929 40.000 16.36 0.00 41.61 2.57
2835 3784 5.560722 TTATGGACCACATACGGATGAAT 57.439 39.130 16.36 0.00 41.61 2.57
2836 3785 3.192541 TGGACCACATACGGATGAATG 57.807 47.619 16.36 2.53 36.48 2.67
2837 3786 2.503765 TGGACCACATACGGATGAATGT 59.496 45.455 16.36 7.89 36.78 2.71
2842 3791 4.737353 CACATACGGATGAATGTGGATG 57.263 45.455 16.36 0.00 45.94 3.51
2843 3792 3.058708 CACATACGGATGAATGTGGATGC 60.059 47.826 16.36 0.00 45.94 3.91
2844 3793 2.998316 TACGGATGAATGTGGATGCA 57.002 45.000 0.00 0.00 0.00 3.96
2845 3794 2.353357 ACGGATGAATGTGGATGCAT 57.647 45.000 0.00 0.00 29.31 3.96
2846 3795 2.658285 ACGGATGAATGTGGATGCATT 58.342 42.857 0.00 0.00 41.28 3.56
2847 3796 3.025978 ACGGATGAATGTGGATGCATTT 58.974 40.909 0.00 0.00 38.98 2.32
2848 3797 3.448301 ACGGATGAATGTGGATGCATTTT 59.552 39.130 0.00 0.00 38.98 1.82
2849 3798 3.799963 CGGATGAATGTGGATGCATTTTG 59.200 43.478 0.00 0.00 38.98 2.44
2850 3799 4.124238 GGATGAATGTGGATGCATTTTGG 58.876 43.478 0.00 0.00 38.98 3.28
2851 3800 4.141892 GGATGAATGTGGATGCATTTTGGA 60.142 41.667 0.00 0.00 38.98 3.53
2852 3801 4.459390 TGAATGTGGATGCATTTTGGAG 57.541 40.909 0.00 0.00 38.98 3.86
2853 3802 3.833650 TGAATGTGGATGCATTTTGGAGT 59.166 39.130 0.00 0.00 38.98 3.85
2854 3803 3.880047 ATGTGGATGCATTTTGGAGTG 57.120 42.857 0.00 0.00 0.00 3.51
2855 3804 2.596346 TGTGGATGCATTTTGGAGTGT 58.404 42.857 0.00 0.00 0.00 3.55
2856 3805 3.760738 TGTGGATGCATTTTGGAGTGTA 58.239 40.909 0.00 0.00 0.00 2.90
2857 3806 3.758023 TGTGGATGCATTTTGGAGTGTAG 59.242 43.478 0.00 0.00 0.00 2.74
2858 3807 4.009675 GTGGATGCATTTTGGAGTGTAGA 58.990 43.478 0.00 0.00 0.00 2.59
2859 3808 4.641989 GTGGATGCATTTTGGAGTGTAGAT 59.358 41.667 0.00 0.00 0.00 1.98
2860 3809 5.126061 GTGGATGCATTTTGGAGTGTAGATT 59.874 40.000 0.00 0.00 0.00 2.40
2861 3810 5.357878 TGGATGCATTTTGGAGTGTAGATTC 59.642 40.000 0.00 0.00 0.00 2.52
2862 3811 5.357878 GGATGCATTTTGGAGTGTAGATTCA 59.642 40.000 0.00 0.00 0.00 2.57
2863 3812 5.627499 TGCATTTTGGAGTGTAGATTCAC 57.373 39.130 0.00 0.00 38.46 3.18
2875 3824 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2876 3825 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2877 3826 4.088823 AGATTCACTCATTTTGCTTCGC 57.911 40.909 0.00 0.00 0.00 4.70
2878 3827 3.503363 AGATTCACTCATTTTGCTTCGCA 59.497 39.130 0.00 0.00 36.47 5.10
2879 3828 3.921119 TTCACTCATTTTGCTTCGCAT 57.079 38.095 0.00 0.00 38.76 4.73
2880 3829 3.206034 TCACTCATTTTGCTTCGCATG 57.794 42.857 0.00 0.00 38.76 4.06
2881 3830 2.553602 TCACTCATTTTGCTTCGCATGT 59.446 40.909 0.00 0.00 38.76 3.21
2882 3831 3.750652 TCACTCATTTTGCTTCGCATGTA 59.249 39.130 0.00 0.00 38.76 2.29
2883 3832 4.093514 CACTCATTTTGCTTCGCATGTAG 58.906 43.478 0.00 0.00 38.76 2.74
2884 3833 3.753272 ACTCATTTTGCTTCGCATGTAGT 59.247 39.130 0.00 0.00 38.76 2.73
2885 3834 4.142816 ACTCATTTTGCTTCGCATGTAGTC 60.143 41.667 0.00 0.00 38.76 2.59
2886 3835 3.126858 TCATTTTGCTTCGCATGTAGTCC 59.873 43.478 0.00 0.00 38.76 3.85
2887 3836 2.177394 TTTGCTTCGCATGTAGTCCA 57.823 45.000 0.00 0.00 38.76 4.02
2888 3837 2.401583 TTGCTTCGCATGTAGTCCAT 57.598 45.000 0.00 0.00 38.76 3.41
2889 3838 3.535280 TTGCTTCGCATGTAGTCCATA 57.465 42.857 0.00 0.00 38.76 2.74
2890 3839 3.097877 TGCTTCGCATGTAGTCCATAG 57.902 47.619 0.00 0.00 31.71 2.23
2891 3840 2.430694 TGCTTCGCATGTAGTCCATAGT 59.569 45.455 0.00 0.00 31.71 2.12
2892 3841 2.797156 GCTTCGCATGTAGTCCATAGTG 59.203 50.000 0.00 0.00 30.71 2.74
2893 3842 3.384668 CTTCGCATGTAGTCCATAGTGG 58.615 50.000 0.00 0.00 39.43 4.00
2894 3843 2.661718 TCGCATGTAGTCCATAGTGGA 58.338 47.619 0.00 0.00 45.98 4.02
2908 3857 7.113658 TCCATAGTGGAATCTCTACAAAGAC 57.886 40.000 0.00 0.00 45.00 3.01
2909 3858 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
2910 3859 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
2911 3860 7.493971 CCATAGTGGAATCTCTACAAAGACTTG 59.506 40.741 0.00 0.00 40.96 3.16
2913 3862 7.540474 AGTGGAATCTCTACAAAGACTTGTA 57.460 36.000 0.00 0.00 44.14 2.41
2914 3863 8.140112 AGTGGAATCTCTACAAAGACTTGTAT 57.860 34.615 0.00 0.00 44.95 2.29
2915 3864 8.598041 AGTGGAATCTCTACAAAGACTTGTATT 58.402 33.333 0.00 0.00 44.95 1.89
2916 3865 9.220767 GTGGAATCTCTACAAAGACTTGTATTT 57.779 33.333 0.00 0.00 44.95 1.40
2922 3871 9.924650 TCTCTACAAAGACTTGTATTTAGGAAC 57.075 33.333 0.00 0.00 44.95 3.62
2923 3872 8.752766 TCTACAAAGACTTGTATTTAGGAACG 57.247 34.615 0.00 0.00 44.95 3.95
2924 3873 6.796705 ACAAAGACTTGTATTTAGGAACGG 57.203 37.500 0.00 0.00 44.14 4.44
2925 3874 6.527423 ACAAAGACTTGTATTTAGGAACGGA 58.473 36.000 0.00 0.00 44.14 4.69
2926 3875 6.649557 ACAAAGACTTGTATTTAGGAACGGAG 59.350 38.462 0.00 0.00 44.14 4.63
2927 3876 5.340439 AGACTTGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2928 3877 4.161754 AGACTTGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2929 3878 4.098894 ACTTGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2930 3879 4.161754 ACTTGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2971 3920 4.329462 TTTGGTTAGCCATTTGGTGAAC 57.671 40.909 0.00 3.33 45.56 3.18
3125 4097 7.053316 TGTCTTGTCATTGGTTGAATTCATT 57.947 32.000 9.40 0.00 35.70 2.57
3169 4141 1.875514 GCTGCAATGACTGTCTGTTCA 59.124 47.619 9.51 1.97 0.00 3.18
3195 4167 1.387747 CGCGCTTGTATTGTGCAACG 61.388 55.000 5.56 0.00 42.39 4.10
3200 4172 0.039617 TTGTATTGTGCAACGCTGGC 60.040 50.000 0.00 0.00 42.39 4.85
3210 4182 0.813184 CAACGCTGGCTGAATCCATT 59.187 50.000 0.00 0.00 35.22 3.16
3315 4287 2.202395 GCCTGCTCAACCTGCCAAA 61.202 57.895 0.00 0.00 0.00 3.28
3338 4310 1.803366 GCAGTTGCTGAGGCTTTGCT 61.803 55.000 12.54 0.00 39.59 3.91
3341 4313 0.240411 GTTGCTGAGGCTTTGCTGAG 59.760 55.000 12.54 0.00 39.59 3.35
3500 4472 1.136529 CAGCGTTCAGATGTGTGTTCG 60.137 52.381 0.00 0.00 0.00 3.95
3628 4859 6.489603 TGGACATTACAACAGGACCATTATT 58.510 36.000 0.00 0.00 0.00 1.40
3629 4860 7.634718 TGGACATTACAACAGGACCATTATTA 58.365 34.615 0.00 0.00 0.00 0.98
4802 6479 6.283544 TCTGAAATATTTTGCATGCCTTCA 57.716 33.333 16.68 10.86 0.00 3.02
4940 6625 2.875933 CAAAGGCGGAACTGTTAAGTCA 59.124 45.455 0.00 0.00 34.77 3.41
4980 6665 4.380843 TTGGTTCAGGTAATGTGGTCAT 57.619 40.909 0.00 0.00 35.59 3.06
5171 7181 8.810041 AGATGAGATTTCAGTGCCTTTAATTTT 58.190 29.630 0.00 0.00 36.61 1.82
5275 7285 1.471119 AAGTACTCGCCGAGAATCCA 58.529 50.000 22.80 0.00 33.32 3.41
5340 7350 1.693627 TTTTTCGCTGGCCAGGTTTA 58.306 45.000 33.46 11.03 0.00 2.01
5546 7588 3.932710 TGTTTCGGCACACAGAGAATATC 59.067 43.478 0.00 0.00 0.00 1.63
5565 7607 3.507162 TCTTGCCCTTGATGAGTGAAA 57.493 42.857 0.00 0.00 0.00 2.69
5578 7620 6.916440 TGATGAGTGAAACCATCAGATTTTG 58.084 36.000 0.00 0.00 44.14 2.44
5584 7626 8.463930 AGTGAAACCATCAGATTTTGTAAAGA 57.536 30.769 0.00 0.00 39.19 2.52
5594 7645 5.049405 CAGATTTTGTAAAGACAGCGGAACT 60.049 40.000 0.00 0.00 36.76 3.01
5617 7668 8.220755 ACTGCATTCTTTTGTAAAGACACTTA 57.779 30.769 1.55 0.00 34.48 2.24
5618 7669 8.129211 ACTGCATTCTTTTGTAAAGACACTTAC 58.871 33.333 1.55 0.00 34.48 2.34
5619 7670 8.220755 TGCATTCTTTTGTAAAGACACTTACT 57.779 30.769 1.55 0.00 34.48 2.24
5620 7671 8.682710 TGCATTCTTTTGTAAAGACACTTACTT 58.317 29.630 1.55 0.00 34.48 2.24
5621 7672 8.958043 GCATTCTTTTGTAAAGACACTTACTTG 58.042 33.333 1.55 0.00 34.48 3.16
5622 7673 9.450807 CATTCTTTTGTAAAGACACTTACTTGG 57.549 33.333 1.55 0.00 34.48 3.61
5623 7674 8.795842 TTCTTTTGTAAAGACACTTACTTGGA 57.204 30.769 1.55 0.00 34.48 3.53
5624 7675 8.433421 TCTTTTGTAAAGACACTTACTTGGAG 57.567 34.615 0.00 0.00 34.48 3.86
5625 7676 8.044908 TCTTTTGTAAAGACACTTACTTGGAGT 58.955 33.333 0.00 0.00 34.48 3.85
5626 7677 8.570068 TTTTGTAAAGACACTTACTTGGAGTT 57.430 30.769 0.00 0.00 34.48 3.01
5667 7718 8.015087 TGTTGATTGTTTTTGAGATAGCTAACG 58.985 33.333 0.00 0.00 0.00 3.18
5703 7754 3.564225 GGTGACACTTACTTGGAGTTTGG 59.436 47.826 5.39 0.00 0.00 3.28
5851 7902 5.049474 GTGTTGTACAGATGAATCAGTTGCA 60.049 40.000 0.00 0.00 0.00 4.08
5875 7926 3.920446 TGCTTACATGTTTCTACTCGCA 58.080 40.909 2.30 0.00 0.00 5.10
6063 8115 1.068748 CGGTAATACGCGTATGAGCCT 60.069 52.381 30.62 19.31 0.00 4.58
6077 8129 2.993008 GCCTGGGCTCATCTCACA 59.007 61.111 4.12 0.00 38.26 3.58
6157 8210 0.884704 AGGAGCGTGCAAATGTTCGT 60.885 50.000 0.00 0.00 0.00 3.85
6186 8239 4.287552 TGGACATTCTAGGACCTTAGACC 58.712 47.826 0.00 0.00 29.67 3.85
6308 8364 2.545526 AGTTTTGCACTCACATCACTCG 59.454 45.455 0.00 0.00 0.00 4.18
6339 8395 5.549742 TCTTGGATGCCAAAAAGTTTCAT 57.450 34.783 0.10 0.00 43.44 2.57
6456 8514 9.849166 TTTACTATTAAGTTGCTAATTTGCCAC 57.151 29.630 9.41 8.56 37.15 5.01
6484 8542 6.381481 TGCAATATGCTACTCTTTTCATGG 57.619 37.500 3.78 0.00 45.31 3.66
6488 8546 8.449397 GCAATATGCTACTCTTTTCATGGATAG 58.551 37.037 0.00 0.00 40.96 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.596082 CCTCGCTCTAGGCTCTAAGC 59.404 60.000 0.00 0.00 41.46 3.09
44 45 2.015456 TCAGCCCAGTGAGAGAGAAA 57.985 50.000 0.00 0.00 0.00 2.52
83 84 3.201708 CCCATTCATTTCTCTCTCCCTGT 59.798 47.826 0.00 0.00 0.00 4.00
106 107 2.224548 CCCCGAGAAAGGAAAACAGAGT 60.225 50.000 0.00 0.00 0.00 3.24
232 277 4.463879 CGGGGAGGTGCAGAGCAG 62.464 72.222 0.00 0.00 40.08 4.24
254 299 1.101635 CCGCCGGTAGACAGAGATCA 61.102 60.000 1.90 0.00 0.00 2.92
298 343 2.040606 GGGAGGGGAGCTGTACCA 59.959 66.667 0.00 0.00 0.00 3.25
329 384 1.566231 CATTGCTAGGGAAGGGGAAGT 59.434 52.381 0.00 0.00 0.00 3.01
330 385 1.133668 CCATTGCTAGGGAAGGGGAAG 60.134 57.143 0.00 0.00 0.00 3.46
331 386 0.926293 CCATTGCTAGGGAAGGGGAA 59.074 55.000 0.00 0.00 0.00 3.97
406 472 9.530633 GATCTATTACGGAGTTTGTTGAATACT 57.469 33.333 0.00 0.00 37.78 2.12
407 473 9.309516 TGATCTATTACGGAGTTTGTTGAATAC 57.690 33.333 0.00 0.00 37.78 1.89
409 475 8.964476 ATGATCTATTACGGAGTTTGTTGAAT 57.036 30.769 0.00 0.00 37.78 2.57
415 481 6.360947 CACGAGATGATCTATTACGGAGTTTG 59.639 42.308 0.00 0.00 37.78 2.93
421 487 5.614923 ACTCACGAGATGATCTATTACGG 57.385 43.478 0.00 0.00 36.48 4.02
430 496 4.578516 CAGAGGAAGTACTCACGAGATGAT 59.421 45.833 0.00 0.00 39.97 2.45
444 510 9.495382 AGACTTATATTTAGGAACAGAGGAAGT 57.505 33.333 0.00 0.00 0.00 3.01
478 659 8.916654 CATCCGTATGTAGTCACTATTGAAATC 58.083 37.037 0.00 0.00 31.90 2.17
577 921 4.650131 CCCTCCGTTCCTAAATAGAAGTCT 59.350 45.833 0.00 0.00 0.00 3.24
583 927 5.139001 AGTACTCCCTCCGTTCCTAAATAG 58.861 45.833 0.00 0.00 0.00 1.73
595 939 2.438800 TGCTGAGTAGTACTCCCTCC 57.561 55.000 24.32 12.03 44.44 4.30
597 941 6.821388 CAATATTTGCTGAGTAGTACTCCCT 58.179 40.000 24.32 0.00 44.44 4.20
758 1102 1.865970 GCTTGCTCTCCAGATGAATCG 59.134 52.381 0.00 0.00 0.00 3.34
810 1157 5.307976 TGATAAATCGGTCCAATCCTCTCAT 59.692 40.000 0.00 0.00 0.00 2.90
862 1209 4.439305 TCACAATTTAGCAGGCATTGTC 57.561 40.909 5.72 0.00 38.75 3.18
892 1239 6.820656 ACAGACAGATTTCAGGATAACATGAC 59.179 38.462 0.00 0.00 36.55 3.06
942 1290 2.300533 GCAACAAACAGCCTGCAAC 58.699 52.632 0.00 0.00 34.87 4.17
1128 1496 2.787249 CGCACTGATTTGGGCTCG 59.213 61.111 0.00 0.00 0.00 5.03
1494 1862 7.344612 GGAATATCCAAATCAAGGTAACCCTTT 59.655 37.037 0.00 0.00 41.59 3.11
1685 2183 3.409570 GCCATATCACAGAGCATCACAT 58.590 45.455 0.00 0.00 37.82 3.21
1823 2323 5.466819 TCTTAGTTACAGTCCAATGTGTCG 58.533 41.667 0.00 0.00 34.56 4.35
2021 2568 7.231317 TGAAAGGCAAAGATCTAAACAGTGATT 59.769 33.333 0.00 0.00 0.00 2.57
2089 2723 2.950781 TGTTACAGATTGCCCAAACCA 58.049 42.857 0.00 0.00 0.00 3.67
2137 2772 2.286067 GCACATTGTCTAGCGATGCTTC 60.286 50.000 11.93 0.00 41.64 3.86
2290 3207 3.191371 CCAACCAGAATAGCAACCACTTC 59.809 47.826 0.00 0.00 0.00 3.01
2420 3338 2.700897 CCCACTCCCAGGTATCTAACAG 59.299 54.545 0.00 0.00 0.00 3.16
2518 3436 7.891498 AAGTTTTGATGGTTACCTTTGTACT 57.109 32.000 2.07 0.00 0.00 2.73
2566 3484 7.768582 TGTCGGCATGGAATATATTAATACAGG 59.231 37.037 0.00 0.00 0.00 4.00
2627 3545 3.028130 TGCTCCGGACATAAGTGTATCA 58.972 45.455 0.00 0.00 39.09 2.15
2628 3546 3.181479 TGTGCTCCGGACATAAGTGTATC 60.181 47.826 0.00 0.00 39.09 2.24
2771 3720 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2772 3721 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2773 3722 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2774 3723 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2775 3724 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2776 3725 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2777 3726 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2794 3743 9.606631 GTCCATAATGAAATCTCTACAAAGACT 57.393 33.333 0.00 0.00 0.00 3.24
2795 3744 8.831550 GGTCCATAATGAAATCTCTACAAAGAC 58.168 37.037 0.00 0.00 0.00 3.01
2796 3745 8.548025 TGGTCCATAATGAAATCTCTACAAAGA 58.452 33.333 0.00 0.00 0.00 2.52
2797 3746 8.616076 GTGGTCCATAATGAAATCTCTACAAAG 58.384 37.037 0.00 0.00 0.00 2.77
2798 3747 8.106462 TGTGGTCCATAATGAAATCTCTACAAA 58.894 33.333 0.00 0.00 0.00 2.83
2799 3748 7.629157 TGTGGTCCATAATGAAATCTCTACAA 58.371 34.615 0.00 0.00 0.00 2.41
2800 3749 7.194112 TGTGGTCCATAATGAAATCTCTACA 57.806 36.000 0.00 0.00 0.00 2.74
2801 3750 9.209175 GTATGTGGTCCATAATGAAATCTCTAC 57.791 37.037 0.00 0.00 37.77 2.59
2802 3751 8.088365 CGTATGTGGTCCATAATGAAATCTCTA 58.912 37.037 0.00 0.00 37.77 2.43
2803 3752 6.931281 CGTATGTGGTCCATAATGAAATCTCT 59.069 38.462 0.00 0.00 37.77 3.10
2804 3753 6.147821 CCGTATGTGGTCCATAATGAAATCTC 59.852 42.308 0.00 0.00 37.77 2.75
2805 3754 5.997746 CCGTATGTGGTCCATAATGAAATCT 59.002 40.000 0.00 0.00 37.77 2.40
2806 3755 5.995282 TCCGTATGTGGTCCATAATGAAATC 59.005 40.000 0.00 0.00 37.77 2.17
2807 3756 5.935945 TCCGTATGTGGTCCATAATGAAAT 58.064 37.500 0.00 0.00 37.77 2.17
2808 3757 5.360649 TCCGTATGTGGTCCATAATGAAA 57.639 39.130 0.00 0.00 37.77 2.69
2809 3758 5.071115 TCATCCGTATGTGGTCCATAATGAA 59.929 40.000 0.00 0.00 37.77 2.57
2810 3759 4.591072 TCATCCGTATGTGGTCCATAATGA 59.409 41.667 0.00 0.00 37.77 2.57
2811 3760 4.893608 TCATCCGTATGTGGTCCATAATG 58.106 43.478 0.00 0.00 37.77 1.90
2812 3761 5.560722 TTCATCCGTATGTGGTCCATAAT 57.439 39.130 0.00 0.00 37.77 1.28
2813 3762 5.163248 ACATTCATCCGTATGTGGTCCATAA 60.163 40.000 0.00 0.00 37.77 1.90
2814 3763 4.346709 ACATTCATCCGTATGTGGTCCATA 59.653 41.667 0.00 0.00 32.48 2.74
2815 3764 3.136443 ACATTCATCCGTATGTGGTCCAT 59.864 43.478 0.00 0.00 32.48 3.41
2816 3765 2.503765 ACATTCATCCGTATGTGGTCCA 59.496 45.455 0.00 0.00 32.48 4.02
2817 3766 2.872245 CACATTCATCCGTATGTGGTCC 59.128 50.000 0.00 0.00 43.47 4.46
2821 3770 3.058708 GCATCCACATTCATCCGTATGTG 60.059 47.826 7.95 7.95 45.52 3.21
2822 3771 3.141398 GCATCCACATTCATCCGTATGT 58.859 45.455 0.00 0.00 33.81 2.29
2823 3772 3.140623 TGCATCCACATTCATCCGTATG 58.859 45.455 0.00 0.00 0.00 2.39
2824 3773 3.490439 TGCATCCACATTCATCCGTAT 57.510 42.857 0.00 0.00 0.00 3.06
2825 3774 2.998316 TGCATCCACATTCATCCGTA 57.002 45.000 0.00 0.00 0.00 4.02
2826 3775 2.353357 ATGCATCCACATTCATCCGT 57.647 45.000 0.00 0.00 0.00 4.69
2827 3776 3.720949 AAATGCATCCACATTCATCCG 57.279 42.857 0.00 0.00 39.32 4.18
2828 3777 4.124238 CCAAAATGCATCCACATTCATCC 58.876 43.478 0.00 0.00 39.32 3.51
2829 3778 5.013568 TCCAAAATGCATCCACATTCATC 57.986 39.130 0.00 0.00 39.32 2.92
2830 3779 4.468510 ACTCCAAAATGCATCCACATTCAT 59.531 37.500 0.00 0.00 39.32 2.57
2831 3780 3.833650 ACTCCAAAATGCATCCACATTCA 59.166 39.130 0.00 0.00 39.32 2.57
2832 3781 4.178540 CACTCCAAAATGCATCCACATTC 58.821 43.478 0.00 0.00 39.32 2.67
2833 3782 3.579586 ACACTCCAAAATGCATCCACATT 59.420 39.130 0.00 0.00 42.01 2.71
2834 3783 3.167485 ACACTCCAAAATGCATCCACAT 58.833 40.909 0.00 0.00 0.00 3.21
2835 3784 2.596346 ACACTCCAAAATGCATCCACA 58.404 42.857 0.00 0.00 0.00 4.17
2836 3785 4.009675 TCTACACTCCAAAATGCATCCAC 58.990 43.478 0.00 0.00 0.00 4.02
2837 3786 4.299586 TCTACACTCCAAAATGCATCCA 57.700 40.909 0.00 0.00 0.00 3.41
2838 3787 5.357878 TGAATCTACACTCCAAAATGCATCC 59.642 40.000 0.00 0.00 0.00 3.51
2839 3788 6.094603 AGTGAATCTACACTCCAAAATGCATC 59.905 38.462 0.00 0.00 46.36 3.91
2840 3789 5.948162 AGTGAATCTACACTCCAAAATGCAT 59.052 36.000 0.00 0.00 46.36 3.96
2841 3790 5.316167 AGTGAATCTACACTCCAAAATGCA 58.684 37.500 0.00 0.00 46.36 3.96
2842 3791 5.886960 AGTGAATCTACACTCCAAAATGC 57.113 39.130 0.00 0.00 46.36 3.56
2852 3801 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2853 3802 6.169419 CGAAGCAAAATGAGTGAATCTACA 57.831 37.500 0.00 0.00 0.00 2.74
2872 3821 3.068165 TCCACTATGGACTACATGCGAAG 59.932 47.826 0.00 0.00 42.67 3.79
2873 3822 3.028130 TCCACTATGGACTACATGCGAA 58.972 45.455 0.00 0.00 42.67 4.70
2874 3823 2.661718 TCCACTATGGACTACATGCGA 58.338 47.619 0.00 0.00 42.67 5.10
2884 3833 6.897966 AGTCTTTGTAGAGATTCCACTATGGA 59.102 38.462 0.00 0.00 46.61 3.41
2885 3834 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
2886 3835 8.037758 ACAAGTCTTTGTAGAGATTCCACTATG 58.962 37.037 0.00 0.00 45.45 2.23
2887 3836 8.140112 ACAAGTCTTTGTAGAGATTCCACTAT 57.860 34.615 0.00 0.00 45.45 2.12
2888 3837 7.540474 ACAAGTCTTTGTAGAGATTCCACTA 57.460 36.000 0.00 0.00 45.45 2.74
2889 3838 6.426646 ACAAGTCTTTGTAGAGATTCCACT 57.573 37.500 0.00 0.00 45.45 4.00
2902 3851 6.092259 CCTCCGTTCCTAAATACAAGTCTTTG 59.908 42.308 0.00 0.00 40.24 2.77
2903 3852 6.171213 CCTCCGTTCCTAAATACAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2904 3853 5.338137 CCCTCCGTTCCTAAATACAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2905 3854 4.161754 CCCTCCGTTCCTAAATACAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2906 3855 4.161001 TCCCTCCGTTCCTAAATACAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2907 3856 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
2908 3857 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
2909 3858 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
2910 3859 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
2911 3860 4.280425 CCTACTCCCTCCGTTCCTAAATAC 59.720 50.000 0.00 0.00 0.00 1.89
2912 3861 4.078980 ACCTACTCCCTCCGTTCCTAAATA 60.079 45.833 0.00 0.00 0.00 1.40
2913 3862 3.306613 CCTACTCCCTCCGTTCCTAAAT 58.693 50.000 0.00 0.00 0.00 1.40
2914 3863 2.043526 ACCTACTCCCTCCGTTCCTAAA 59.956 50.000 0.00 0.00 0.00 1.85
2915 3864 1.642762 ACCTACTCCCTCCGTTCCTAA 59.357 52.381 0.00 0.00 0.00 2.69
2916 3865 1.302907 ACCTACTCCCTCCGTTCCTA 58.697 55.000 0.00 0.00 0.00 2.94
2917 3866 1.214923 CTACCTACTCCCTCCGTTCCT 59.785 57.143 0.00 0.00 0.00 3.36
2918 3867 1.213926 TCTACCTACTCCCTCCGTTCC 59.786 57.143 0.00 0.00 0.00 3.62
2919 3868 2.725221 TCTACCTACTCCCTCCGTTC 57.275 55.000 0.00 0.00 0.00 3.95
2920 3869 3.053095 TGATTCTACCTACTCCCTCCGTT 60.053 47.826 0.00 0.00 0.00 4.44
2921 3870 2.512896 TGATTCTACCTACTCCCTCCGT 59.487 50.000 0.00 0.00 0.00 4.69
2922 3871 3.150767 CTGATTCTACCTACTCCCTCCG 58.849 54.545 0.00 0.00 0.00 4.63
2923 3872 4.456662 TCTGATTCTACCTACTCCCTCC 57.543 50.000 0.00 0.00 0.00 4.30
2924 3873 5.451354 ACTTCTGATTCTACCTACTCCCTC 58.549 45.833 0.00 0.00 0.00 4.30
2925 3874 5.475398 ACTTCTGATTCTACCTACTCCCT 57.525 43.478 0.00 0.00 0.00 4.20
2926 3875 7.842887 ATAACTTCTGATTCTACCTACTCCC 57.157 40.000 0.00 0.00 0.00 4.30
2927 3876 9.535878 CAAATAACTTCTGATTCTACCTACTCC 57.464 37.037 0.00 0.00 0.00 3.85
2928 3877 9.535878 CCAAATAACTTCTGATTCTACCTACTC 57.464 37.037 0.00 0.00 0.00 2.59
2929 3878 9.047947 ACCAAATAACTTCTGATTCTACCTACT 57.952 33.333 0.00 0.00 0.00 2.57
2930 3879 9.668497 AACCAAATAACTTCTGATTCTACCTAC 57.332 33.333 0.00 0.00 0.00 3.18
3125 4097 6.016527 GCATGCATGAAGGATTTTCATCTAGA 60.017 38.462 30.64 0.00 37.06 2.43
3195 4167 2.372264 TCAAGAATGGATTCAGCCAGC 58.628 47.619 2.32 0.00 42.15 4.85
3200 4172 6.346896 TCAGACTCATCAAGAATGGATTCAG 58.653 40.000 2.32 0.00 39.23 3.02
3210 4182 8.102676 TGTTTCCATATTTCAGACTCATCAAGA 58.897 33.333 0.00 0.00 0.00 3.02
3272 4244 4.021559 CCATCAAGTGGCCATGCA 57.978 55.556 9.72 0.00 42.12 3.96
3315 4287 2.672307 GCCTCAGCAACTGCAGCT 60.672 61.111 15.27 2.71 45.16 4.24
3338 4310 1.214175 TGCAAGAAAACAGGGGACTCA 59.786 47.619 0.00 0.00 40.21 3.41
3341 4313 3.321968 AGAAATGCAAGAAAACAGGGGAC 59.678 43.478 0.00 0.00 0.00 4.46
3423 4395 1.032014 ACACAACATGTCCAAGGCAC 58.968 50.000 0.00 0.00 36.54 5.01
3628 4859 9.444600 ACTCAGAAGTTATCGCCTTTTAAAATA 57.555 29.630 0.09 0.00 28.74 1.40
3629 4860 8.336801 ACTCAGAAGTTATCGCCTTTTAAAAT 57.663 30.769 0.09 0.00 28.74 1.82
3780 5066 2.003301 GTGAAGAAGAATCTGTCGGGC 58.997 52.381 0.00 0.00 35.59 6.13
4940 6625 6.882768 ACCAAATCTTTCTCCTCTATCACT 57.117 37.500 0.00 0.00 0.00 3.41
4980 6665 6.931838 ACTGTGATTCGAAATGGTTCTAGTA 58.068 36.000 0.00 0.00 0.00 1.82
5140 7150 4.080695 AGGCACTGAAATCTCATCTGCTAA 60.081 41.667 0.32 0.00 37.18 3.09
5275 7285 2.744202 CCGATACTGCTCAAGTTGCTTT 59.256 45.455 0.00 0.00 40.56 3.51
5340 7350 7.341256 ACACAGCTCCAGATTCAAAAATATCAT 59.659 33.333 0.00 0.00 0.00 2.45
5546 7588 2.229784 GGTTTCACTCATCAAGGGCAAG 59.770 50.000 0.00 0.00 0.00 4.01
5565 7607 5.106555 CGCTGTCTTTACAAAATCTGATGGT 60.107 40.000 0.00 0.00 34.49 3.55
5576 7618 1.871039 GCAGTTCCGCTGTCTTTACAA 59.129 47.619 0.00 0.00 46.64 2.41
5577 7619 1.202592 TGCAGTTCCGCTGTCTTTACA 60.203 47.619 0.00 0.00 46.64 2.41
5578 7620 1.508632 TGCAGTTCCGCTGTCTTTAC 58.491 50.000 0.00 0.00 46.64 2.01
5584 7626 1.609208 AAAGAATGCAGTTCCGCTGT 58.391 45.000 0.00 0.00 46.64 4.40
5594 7645 8.220755 AGTAAGTGTCTTTACAAAAGAATGCA 57.779 30.769 3.77 0.00 37.36 3.96
5667 7718 0.733150 GTCACCGCTTGGAATAAGCC 59.267 55.000 6.11 0.00 40.02 4.35
5703 7754 5.578727 AGAGAGCGAAATGTAATCAACACTC 59.421 40.000 0.00 0.00 42.09 3.51
5851 7902 6.280643 TGCGAGTAGAAACATGTAAGCATAT 58.719 36.000 0.00 0.00 33.30 1.78
6036 8088 5.965202 TCATACGCGTATTACCGAAAATTG 58.035 37.500 28.35 14.47 0.00 2.32
6063 8115 2.506644 TCATCAATGTGAGATGAGCCCA 59.493 45.455 2.00 0.00 44.98 5.36
6102 8155 8.273780 AGCATCTTCGATGATTCTTTTTACTT 57.726 30.769 10.88 0.00 0.00 2.24
6157 8210 3.244770 GGTCCTAGAATGTCCAAACACCA 60.245 47.826 0.00 0.00 38.48 4.17
6195 8248 3.914426 AAGAGCACTATTTGGATCCGT 57.086 42.857 7.39 0.00 0.00 4.69
6219 8274 7.920160 AAAAATGGCTTCAAAAGAAACTTCA 57.080 28.000 0.00 0.00 0.00 3.02
6308 8364 1.729881 GCATCCAAGATGCCCGAAC 59.270 57.895 16.90 0.00 39.01 3.95
6383 8439 1.224592 GGATTCGGTGCCTGGTCAT 59.775 57.895 0.00 0.00 0.00 3.06
6384 8440 2.220586 TGGATTCGGTGCCTGGTCA 61.221 57.895 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.