Multiple sequence alignment - TraesCS5A01G176800

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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 TraesCS5A01G176800 chr5A 100.000 6194 0 0 1 6194 372596439 372590246 0.000000e+00 11439.0
1 TraesCS5A01G176800 chr5A 92.857 70 5 0 5932 6001 563845384 563845315 1.100000e-17 102.0
2 TraesCS5A01G176800 chr5D 95.575 3706 68 22 2273 5933 280380353 280384007 0.000000e+00 5847.0
3 TraesCS5A01G176800 chr5D 98.098 1525 28 1 729 2252 280378837 280380361 0.000000e+00 2654.0
4 TraesCS5A01G176800 chr5D 90.769 195 18 0 6000 6194 313096637 313096443 1.710000e-65 261.0
5 TraesCS5A01G176800 chr5D 90.306 196 18 1 6000 6194 55831999 55832194 7.970000e-64 255.0
6 TraesCS5A01G176800 chr5B 94.234 1873 63 11 3949 5802 318173354 318175200 0.000000e+00 2819.0
7 TraesCS5A01G176800 chr5B 95.901 1537 54 6 752 2284 318169679 318171210 0.000000e+00 2481.0
8 TraesCS5A01G176800 chr5B 91.987 1560 86 9 2372 3905 318171228 318172774 0.000000e+00 2152.0
9 TraesCS5A01G176800 chr5B 91.216 444 30 5 1 439 318168401 318168840 4.130000e-166 595.0
10 TraesCS5A01G176800 chr5B 93.089 246 15 2 438 682 318169234 318169478 5.900000e-95 359.0
11 TraesCS5A01G176800 chr5B 90.863 197 16 2 6000 6194 523380299 523380103 4.760000e-66 263.0
12 TraesCS5A01G176800 chr5B 86.713 143 17 2 2792 2933 652099624 652099483 2.310000e-34 158.0
13 TraesCS5A01G176800 chr5B 86.713 143 17 2 2792 2933 652368653 652368512 2.310000e-34 158.0
14 TraesCS5A01G176800 chr5B 93.023 86 3 1 5848 5933 318175214 318175296 8.430000e-24 122.0
15 TraesCS5A01G176800 chr2B 87.465 718 78 9 3514 4223 705205808 705205095 0.000000e+00 817.0
16 TraesCS5A01G176800 chr2B 95.588 68 3 0 5932 5999 738336770 738336703 6.560000e-20 110.0
17 TraesCS5A01G176800 chr4A 84.408 667 70 16 3515 4178 708628073 708627438 5.270000e-175 625.0
18 TraesCS5A01G176800 chr4A 88.976 127 12 2 2792 2917 590222577 590222452 8.310000e-34 156.0
19 TraesCS5A01G176800 chr4B 84.227 653 68 15 3530 4178 600524867 600524246 2.470000e-168 603.0
20 TraesCS5A01G176800 chr4B 89.764 127 11 2 2792 2917 22850698 22850823 1.790000e-35 161.0
21 TraesCS5A01G176800 chr4B 85.437 103 12 1 4177 4279 600524211 600524112 3.050000e-18 104.0
22 TraesCS5A01G176800 chr3D 91.667 192 16 0 6003 6194 534171020 534171211 3.680000e-67 267.0
23 TraesCS5A01G176800 chr3D 87.324 142 17 1 2792 2933 385508644 385508784 1.790000e-35 161.0
24 TraesCS5A01G176800 chr3D 94.366 71 4 0 5929 5999 94490528 94490598 6.560000e-20 110.0
25 TraesCS5A01G176800 chr3D 91.892 74 6 0 5922 5995 30972023 30972096 3.050000e-18 104.0
26 TraesCS5A01G176800 chrUn 90.404 198 15 3 6000 6194 134356788 134356984 2.220000e-64 257.0
27 TraesCS5A01G176800 chr6A 90.355 197 17 2 6000 6194 588181498 588181694 2.220000e-64 257.0
28 TraesCS5A01G176800 chr6A 80.128 156 27 4 3087 3240 205946360 205946207 5.070000e-21 113.0
29 TraesCS5A01G176800 chr6A 94.444 72 4 0 5928 5999 16292192 16292263 1.830000e-20 111.0
30 TraesCS5A01G176800 chr6A 96.226 53 1 1 345 397 58374513 58374564 1.110000e-12 86.1
31 TraesCS5A01G176800 chr3B 90.256 195 19 0 6000 6194 706250884 706251078 7.970000e-64 255.0
32 TraesCS5A01G176800 chr3B 88.732 71 7 1 5932 6002 487563755 487563686 1.110000e-12 86.1
33 TraesCS5A01G176800 chr1A 90.625 192 16 2 6002 6192 497200030 497200220 2.870000e-63 254.0
34 TraesCS5A01G176800 chr1D 89.796 196 19 1 6000 6194 61479768 61479573 3.710000e-62 250.0
35 TraesCS5A01G176800 chr1D 95.775 71 3 0 5929 5999 126186055 126186125 1.410000e-21 115.0
36 TraesCS5A01G176800 chr2A 87.500 136 15 1 2798 2933 136343159 136343026 8.310000e-34 156.0
37 TraesCS5A01G176800 chr2A 94.203 69 3 1 5932 6000 585923616 585923549 3.050000e-18 104.0
38 TraesCS5A01G176800 chr4D 86.719 128 17 0 2792 2919 458888837 458888710 6.470000e-30 143.0
39 TraesCS5A01G176800 chr4D 94.366 71 4 0 5929 5999 420944973 420945043 6.560000e-20 110.0
40 TraesCS5A01G176800 chr4D 94.203 69 3 1 5932 6000 498881133 498881066 3.050000e-18 104.0
41 TraesCS5A01G176800 chr7D 95.588 68 3 0 5932 5999 37918710 37918643 6.560000e-20 110.0
42 TraesCS5A01G176800 chr7D 85.149 101 15 0 4177 4277 69082518 69082418 3.050000e-18 104.0
43 TraesCS5A01G176800 chr7D 91.803 61 5 0 5941 6001 523398501 523398561 1.110000e-12 86.1
44 TraesCS5A01G176800 chr7B 94.366 71 4 0 5929 5999 180034656 180034726 6.560000e-20 110.0
45 TraesCS5A01G176800 chr7A 79.618 157 28 4 3086 3240 249082496 249082650 6.560000e-20 110.0
46 TraesCS5A01G176800 chr6D 95.588 68 3 0 5932 5999 41947885 41947818 6.560000e-20 110.0
47 TraesCS5A01G176800 chr6D 91.781 73 5 1 5928 6000 38154047 38153976 3.950000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G176800 chr5A 372590246 372596439 6193 True 11439.000000 11439 100.000000 1 6194 1 chr5A.!!$R1 6193
1 TraesCS5A01G176800 chr5D 280378837 280384007 5170 False 4250.500000 5847 96.836500 729 5933 2 chr5D.!!$F2 5204
2 TraesCS5A01G176800 chr5B 318168401 318175296 6895 False 1421.333333 2819 93.241667 1 5933 6 chr5B.!!$F1 5932
3 TraesCS5A01G176800 chr2B 705205095 705205808 713 True 817.000000 817 87.465000 3514 4223 1 chr2B.!!$R1 709
4 TraesCS5A01G176800 chr4A 708627438 708628073 635 True 625.000000 625 84.408000 3515 4178 1 chr4A.!!$R2 663
5 TraesCS5A01G176800 chr4B 600524112 600524867 755 True 353.500000 603 84.832000 3530 4279 2 chr4B.!!$R1 749

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
566 967 0.107165 GGGGAAGGAAAGATGGACGG 60.107 60.000 0.00 0.0 0.00 4.79 F
816 1380 0.179129 GGCGACGGGAATCGAAAGTA 60.179 55.000 0.00 0.0 45.13 2.24 F
1289 1853 0.530870 GCGGGTGCTTAGGAGATGTC 60.531 60.000 0.00 0.0 38.39 3.06 F
2261 2828 0.987294 AACATGGTCTAGGCAGCTGT 59.013 50.000 16.64 0.0 0.00 4.40 F
2360 2938 5.163258 GCATCCAAGGGAGAAGAAGAATAGA 60.163 44.000 0.00 0.0 34.05 1.98 F
3917 4574 4.764679 ATTGCGTGTATGCTTCTTTGAA 57.235 36.364 0.00 0.0 35.36 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 2213 0.257328 TTGTCTTTGGGCAGTCACCA 59.743 50.000 0.00 0.0 35.88 4.17 R
2302 2869 1.595093 GCATTTTACGGGGCAGCAGT 61.595 55.000 0.00 0.0 0.00 4.40 R
2363 2941 4.777896 TCTACTAAGCAGTTCAATCACCCT 59.222 41.667 0.00 0.0 36.14 4.34 R
3362 3985 1.963515 AGGTGGCCTTTTTACAGCAAG 59.036 47.619 3.32 0.0 35.24 4.01 R
3932 4589 2.053244 AGCAGCCTCATAGCATTACCT 58.947 47.619 0.00 0.0 34.23 3.08 R
5810 7094 0.174389 TGATCTGGACGAGAAGCTGC 59.826 55.000 0.00 0.0 33.12 5.25 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 1.448922 GGTACCGTTGTTGGCAGCAA 61.449 55.000 13.01 13.01 0.00 3.91
34 35 0.317519 GTACCGTTGTTGGCAGCAAC 60.318 55.000 30.05 30.05 41.81 4.17
35 36 0.748367 TACCGTTGTTGGCAGCAACA 60.748 50.000 35.32 20.53 44.49 3.33
36 37 1.588667 CCGTTGTTGGCAGCAACAC 60.589 57.895 35.32 18.88 43.76 3.32
37 38 1.433064 CGTTGTTGGCAGCAACACT 59.567 52.632 35.32 0.00 43.76 3.55
46 47 4.033894 AGCAACACTGACAGACGC 57.966 55.556 10.08 5.82 0.00 5.19
47 48 1.951130 AGCAACACTGACAGACGCG 60.951 57.895 10.08 3.53 0.00 6.01
52 53 0.169230 ACACTGACAGACGCGAGATC 59.831 55.000 15.93 0.00 0.00 2.75
54 55 0.960861 ACTGACAGACGCGAGATCCA 60.961 55.000 15.93 3.99 0.00 3.41
55 56 0.524392 CTGACAGACGCGAGATCCAC 60.524 60.000 15.93 0.00 0.00 4.02
87 88 1.466866 CGACTAATGCGACCTGACGAA 60.467 52.381 0.00 0.00 35.09 3.85
100 101 0.323629 TGACGAAAGATGTGACCCCC 59.676 55.000 0.00 0.00 0.00 5.40
212 216 1.918262 ACATGCTTCAAGATGGGGAGA 59.082 47.619 0.00 0.00 0.00 3.71
215 219 0.182299 GCTTCAAGATGGGGAGAGGG 59.818 60.000 0.00 0.00 0.00 4.30
218 222 0.621571 TCAAGATGGGGAGAGGGTGG 60.622 60.000 0.00 0.00 0.00 4.61
225 229 1.341156 GGGGAGAGGGTGGAGATGTG 61.341 65.000 0.00 0.00 0.00 3.21
233 237 0.674895 GGTGGAGATGTGGTGCAGTC 60.675 60.000 0.00 0.00 0.00 3.51
248 252 2.512515 GTCCCCACTCGCTGATGC 60.513 66.667 0.00 0.00 0.00 3.91
249 253 3.785859 TCCCCACTCGCTGATGCC 61.786 66.667 0.00 0.00 35.36 4.40
300 304 0.610232 GAGGATGTGCAAAGCTGGGT 60.610 55.000 0.00 0.00 0.00 4.51
302 306 1.075374 AGGATGTGCAAAGCTGGGTTA 59.925 47.619 0.00 0.00 0.00 2.85
323 327 1.439543 GGGTGCTGGGATAGGAAGAT 58.560 55.000 0.00 0.00 0.00 2.40
324 328 2.621070 GGGTGCTGGGATAGGAAGATA 58.379 52.381 0.00 0.00 0.00 1.98
325 329 2.303311 GGGTGCTGGGATAGGAAGATAC 59.697 54.545 0.00 0.00 0.00 2.24
326 330 2.972713 GGTGCTGGGATAGGAAGATACA 59.027 50.000 0.00 0.00 0.00 2.29
327 331 3.584848 GGTGCTGGGATAGGAAGATACAT 59.415 47.826 0.00 0.00 0.00 2.29
328 332 4.777896 GGTGCTGGGATAGGAAGATACATA 59.222 45.833 0.00 0.00 0.00 2.29
329 333 5.105146 GGTGCTGGGATAGGAAGATACATAG 60.105 48.000 0.00 0.00 0.00 2.23
330 334 5.026121 TGCTGGGATAGGAAGATACATAGG 58.974 45.833 0.00 0.00 0.00 2.57
331 335 5.026790 GCTGGGATAGGAAGATACATAGGT 58.973 45.833 0.00 0.00 0.00 3.08
336 342 9.455144 TGGGATAGGAAGATACATAGGTAAAAA 57.545 33.333 0.00 0.00 32.19 1.94
363 369 2.820899 AAATTCCTGGGCGGGCCATT 62.821 55.000 24.64 12.49 37.98 3.16
413 419 2.553904 CCCTGCCTTTGAGTCTGTCAAT 60.554 50.000 0.00 0.00 44.89 2.57
418 424 3.743521 CCTTTGAGTCTGTCAATCCACA 58.256 45.455 0.00 0.00 44.89 4.17
421 427 4.356405 TTGAGTCTGTCAATCCACACAT 57.644 40.909 0.00 0.00 40.45 3.21
426 432 5.620206 AGTCTGTCAATCCACACATACAAA 58.380 37.500 0.00 0.00 0.00 2.83
481 882 2.628178 TGAAGCAAACTCGAGGAGAAGA 59.372 45.455 18.41 0.00 33.32 2.87
497 898 4.636206 GGAGAAGAACACAAGAAACACACT 59.364 41.667 0.00 0.00 0.00 3.55
498 899 5.447818 GGAGAAGAACACAAGAAACACACTG 60.448 44.000 0.00 0.00 0.00 3.66
533 934 5.047188 CCATGTGGTTTGTAACTGGTTTTC 58.953 41.667 0.00 0.00 0.00 2.29
536 937 6.687081 TGTGGTTTGTAACTGGTTTTCTAG 57.313 37.500 0.00 0.00 34.46 2.43
537 938 6.416415 TGTGGTTTGTAACTGGTTTTCTAGA 58.584 36.000 0.00 0.00 32.56 2.43
538 939 6.540914 TGTGGTTTGTAACTGGTTTTCTAGAG 59.459 38.462 0.00 0.00 32.56 2.43
539 940 6.541278 GTGGTTTGTAACTGGTTTTCTAGAGT 59.459 38.462 0.00 0.00 32.56 3.24
540 941 6.540914 TGGTTTGTAACTGGTTTTCTAGAGTG 59.459 38.462 0.00 0.00 32.56 3.51
541 942 6.764560 GGTTTGTAACTGGTTTTCTAGAGTGA 59.235 38.462 0.00 0.00 32.56 3.41
542 943 7.041984 GGTTTGTAACTGGTTTTCTAGAGTGAG 60.042 40.741 0.00 0.00 32.56 3.51
562 963 4.019858 GAGAAAAGGGGAAGGAAAGATGG 58.980 47.826 0.00 0.00 0.00 3.51
563 964 3.662642 AGAAAAGGGGAAGGAAAGATGGA 59.337 43.478 0.00 0.00 0.00 3.41
566 967 0.107165 GGGGAAGGAAAGATGGACGG 60.107 60.000 0.00 0.00 0.00 4.79
687 1250 8.935844 CCTTTGGTTGATTTTAAAATAGAAGGC 58.064 33.333 13.34 1.29 0.00 4.35
816 1380 0.179129 GGCGACGGGAATCGAAAGTA 60.179 55.000 0.00 0.00 45.13 2.24
928 1492 3.902881 AGAATCTTCCAGAATCAGCGT 57.097 42.857 0.00 0.00 0.00 5.07
1177 1741 2.498726 CGCAGCTCCCTCTCCTTC 59.501 66.667 0.00 0.00 0.00 3.46
1289 1853 0.530870 GCGGGTGCTTAGGAGATGTC 60.531 60.000 0.00 0.00 38.39 3.06
1371 1935 9.996554 TTCTGATTGAGATTTACTAGTGTTTGA 57.003 29.630 5.39 0.00 0.00 2.69
1493 2057 9.048446 CATGTCTTTTTCAAGGAAAATGATGTT 57.952 29.630 17.43 7.80 42.86 2.71
2261 2828 0.987294 AACATGGTCTAGGCAGCTGT 59.013 50.000 16.64 0.00 0.00 4.40
2302 2869 8.726988 GCTGTGGTAAGACAAAATCAATACTAA 58.273 33.333 0.00 0.00 0.00 2.24
2360 2938 5.163258 GCATCCAAGGGAGAAGAAGAATAGA 60.163 44.000 0.00 0.00 34.05 1.98
2361 2939 6.633583 GCATCCAAGGGAGAAGAAGAATAGAA 60.634 42.308 0.00 0.00 34.05 2.10
2363 2941 8.654997 CATCCAAGGGAGAAGAAGAATAGAATA 58.345 37.037 0.00 0.00 34.05 1.75
2364 2942 8.256356 TCCAAGGGAGAAGAAGAATAGAATAG 57.744 38.462 0.00 0.00 0.00 1.73
2365 2943 7.291182 TCCAAGGGAGAAGAAGAATAGAATAGG 59.709 40.741 0.00 0.00 0.00 2.57
2366 2944 7.449247 CAAGGGAGAAGAAGAATAGAATAGGG 58.551 42.308 0.00 0.00 0.00 3.53
2367 2945 6.698670 AGGGAGAAGAAGAATAGAATAGGGT 58.301 40.000 0.00 0.00 0.00 4.34
2368 2946 6.556874 AGGGAGAAGAAGAATAGAATAGGGTG 59.443 42.308 0.00 0.00 0.00 4.61
2370 2948 7.236640 GGGAGAAGAAGAATAGAATAGGGTGAT 59.763 40.741 0.00 0.00 0.00 3.06
2402 2999 8.103305 TGCTTAGTAGACAATTGAGGAGAATTT 58.897 33.333 13.59 0.00 0.00 1.82
2513 3110 8.952278 GTCTCTATGACTTCTCTCTGTTTTAGA 58.048 37.037 0.00 0.00 42.21 2.10
2654 3275 6.540189 ACCGAAATGATTGAATGGACTAGAAG 59.460 38.462 0.00 0.00 0.00 2.85
3441 4064 8.193438 GCTGAAAGATTTATCTTATGGCTGTTT 58.807 33.333 5.47 0.00 45.83 2.83
3555 4178 8.753497 ATTCCCTAATCCAAATTCAGTAGTTC 57.247 34.615 0.00 0.00 0.00 3.01
3601 4224 6.908825 TCAAGTTACATTCTGTGCCATTTAC 58.091 36.000 0.00 0.00 0.00 2.01
3905 4562 7.530863 TCAATGTTGCTTTTATATTGCGTGTA 58.469 30.769 0.00 0.00 0.00 2.90
3906 4563 8.187480 TCAATGTTGCTTTTATATTGCGTGTAT 58.813 29.630 0.00 0.00 0.00 2.29
3907 4564 7.912949 ATGTTGCTTTTATATTGCGTGTATG 57.087 32.000 0.00 0.00 0.00 2.39
3908 4565 5.741510 TGTTGCTTTTATATTGCGTGTATGC 59.258 36.000 0.00 0.00 0.00 3.14
3909 4566 5.749596 TGCTTTTATATTGCGTGTATGCT 57.250 34.783 0.00 0.00 35.36 3.79
3910 4567 6.130298 TGCTTTTATATTGCGTGTATGCTT 57.870 33.333 0.00 0.00 35.36 3.91
3911 4568 6.198687 TGCTTTTATATTGCGTGTATGCTTC 58.801 36.000 0.00 0.00 35.36 3.86
3912 4569 6.038161 TGCTTTTATATTGCGTGTATGCTTCT 59.962 34.615 0.00 0.00 35.36 2.85
3913 4570 6.912591 GCTTTTATATTGCGTGTATGCTTCTT 59.087 34.615 0.00 0.00 35.36 2.52
3914 4571 7.432252 GCTTTTATATTGCGTGTATGCTTCTTT 59.568 33.333 0.00 0.00 35.36 2.52
3915 4572 8.613613 TTTTATATTGCGTGTATGCTTCTTTG 57.386 30.769 0.00 0.00 35.36 2.77
3916 4573 7.546778 TTATATTGCGTGTATGCTTCTTTGA 57.453 32.000 0.00 0.00 35.36 2.69
3917 4574 4.764679 ATTGCGTGTATGCTTCTTTGAA 57.235 36.364 0.00 0.00 35.36 2.69
3918 4575 4.764679 TTGCGTGTATGCTTCTTTGAAT 57.235 36.364 0.00 0.00 35.36 2.57
3919 4576 4.764679 TGCGTGTATGCTTCTTTGAATT 57.235 36.364 0.00 0.00 35.36 2.17
3920 4577 5.871465 TGCGTGTATGCTTCTTTGAATTA 57.129 34.783 0.00 0.00 35.36 1.40
3921 4578 6.247727 TGCGTGTATGCTTCTTTGAATTAA 57.752 33.333 0.00 0.00 35.36 1.40
3922 4579 6.673106 TGCGTGTATGCTTCTTTGAATTAAA 58.327 32.000 0.00 0.00 35.36 1.52
3923 4580 7.142021 TGCGTGTATGCTTCTTTGAATTAAAA 58.858 30.769 0.00 0.00 35.36 1.52
3924 4581 7.812191 TGCGTGTATGCTTCTTTGAATTAAAAT 59.188 29.630 0.00 0.00 35.36 1.82
3925 4582 8.313931 GCGTGTATGCTTCTTTGAATTAAAATC 58.686 33.333 0.00 0.00 0.00 2.17
3926 4583 9.559958 CGTGTATGCTTCTTTGAATTAAAATCT 57.440 29.630 0.00 0.00 0.00 2.40
3955 5177 5.026121 AGGTAATGCTATGAGGCTGCTATA 58.974 41.667 0.00 0.00 0.00 1.31
4180 5404 5.221541 CCCCCAACAGATCAGAGTAATAGAC 60.222 48.000 0.00 0.00 0.00 2.59
4303 5563 2.249844 TCCTCTTTGGTGGAAACGTC 57.750 50.000 0.00 0.00 37.07 4.34
4647 5907 5.068198 TCAAAGCTTTTGATTCTCTGTTGCT 59.932 36.000 9.53 0.00 0.00 3.91
4678 5938 8.518702 TGCTGCTTTGTATGTAATTATGTTCAA 58.481 29.630 0.00 0.00 0.00 2.69
4890 6156 1.272212 TGAATTTTTCTGGCGGCCTTC 59.728 47.619 21.46 13.61 0.00 3.46
5094 6360 5.414454 TCATGACTTGTACCATTACCTTTGC 59.586 40.000 0.00 0.00 0.00 3.68
5223 6489 1.579964 ATGGCATGTGACACGCTGTG 61.580 55.000 2.96 7.07 34.80 3.66
5408 6674 0.398098 TCGGTATCCACTTCTCCCCC 60.398 60.000 0.00 0.00 0.00 5.40
5583 6850 4.464597 TGTGTGCCTTGAGTTTACCTTTTT 59.535 37.500 0.00 0.00 0.00 1.94
5652 6925 4.225942 TGCATGGAAGTATTCTGAGGAAGT 59.774 41.667 0.00 0.00 46.56 3.01
5717 7001 2.146342 CGATTGCTGTGGAAGTGTCTT 58.854 47.619 0.00 0.00 0.00 3.01
5718 7002 3.244078 ACGATTGCTGTGGAAGTGTCTTA 60.244 43.478 0.00 0.00 0.00 2.10
5756 7040 0.741915 TTGCGTTCCCAACCTGTTTC 59.258 50.000 0.00 0.00 0.00 2.78
5805 7089 4.864334 CCCAGGTGCATCTCGCCC 62.864 72.222 0.00 0.00 46.60 6.13
5806 7090 4.100084 CCAGGTGCATCTCGCCCA 62.100 66.667 0.00 0.00 46.60 5.36
5807 7091 2.513204 CAGGTGCATCTCGCCCAG 60.513 66.667 0.00 0.00 46.60 4.45
5809 7093 4.783621 GGTGCATCTCGCCCAGCA 62.784 66.667 0.00 0.00 41.33 4.41
5810 7094 3.200593 GTGCATCTCGCCCAGCAG 61.201 66.667 0.00 0.00 41.33 4.24
5813 7097 2.895865 CATCTCGCCCAGCAGCAG 60.896 66.667 0.00 0.00 0.00 4.24
5864 7148 4.641396 TCAAACAATCGACTGATCAACCT 58.359 39.130 0.00 0.00 32.24 3.50
5874 7158 2.373169 ACTGATCAACCTGCAAAGGAGA 59.627 45.455 0.00 0.00 0.00 3.71
5933 7217 4.020751 AGCAGATCAACTAGCAAACTGAGA 60.021 41.667 0.00 0.00 0.00 3.27
5934 7218 4.329528 GCAGATCAACTAGCAAACTGAGAG 59.670 45.833 0.00 0.00 0.00 3.20
5935 7219 4.329528 CAGATCAACTAGCAAACTGAGAGC 59.670 45.833 0.00 0.00 0.00 4.09
5936 7220 3.751479 TCAACTAGCAAACTGAGAGCA 57.249 42.857 0.00 0.00 0.00 4.26
5937 7221 4.277515 TCAACTAGCAAACTGAGAGCAT 57.722 40.909 0.00 0.00 0.00 3.79
5938 7222 4.248859 TCAACTAGCAAACTGAGAGCATC 58.751 43.478 0.00 0.00 0.00 3.91
5951 7235 1.703411 GAGCATCTCTAGCAGACCCT 58.297 55.000 0.00 0.00 32.26 4.34
5952 7236 1.340889 GAGCATCTCTAGCAGACCCTG 59.659 57.143 0.00 0.00 32.26 4.45
5961 7245 2.825836 CAGACCCTGCATTCCGCC 60.826 66.667 0.00 0.00 41.33 6.13
5962 7246 4.473520 AGACCCTGCATTCCGCCG 62.474 66.667 0.00 0.00 41.33 6.46
5987 7271 0.223513 CAAAACGCGTTTGCAGTTCG 59.776 50.000 35.31 15.11 40.25 3.95
5988 7272 1.468340 AAAACGCGTTTGCAGTTCGC 61.468 50.000 35.31 17.67 45.28 4.70
5991 7275 4.007940 GCGTTTGCAGTTCGCGGA 62.008 61.111 6.13 0.00 46.97 5.54
5992 7276 2.629210 CGTTTGCAGTTCGCGGAA 59.371 55.556 6.13 0.00 46.97 4.30
5993 7277 1.010574 CGTTTGCAGTTCGCGGAAA 60.011 52.632 6.13 0.00 46.97 3.13
5994 7278 0.590230 CGTTTGCAGTTCGCGGAAAA 60.590 50.000 6.13 0.00 46.97 2.29
5995 7279 1.551145 GTTTGCAGTTCGCGGAAAAA 58.449 45.000 6.13 0.00 46.97 1.94
5996 7280 1.254313 GTTTGCAGTTCGCGGAAAAAC 59.746 47.619 6.13 2.77 46.97 2.43
5997 7281 0.590230 TTGCAGTTCGCGGAAAAACG 60.590 50.000 6.13 1.38 46.97 3.60
5998 7282 1.724581 GCAGTTCGCGGAAAAACGG 60.725 57.895 6.13 5.16 0.00 4.44
5999 7283 1.082366 CAGTTCGCGGAAAAACGGG 60.082 57.895 6.13 0.00 46.53 5.28
6000 7284 1.524393 AGTTCGCGGAAAAACGGGT 60.524 52.632 6.13 0.00 45.53 5.28
6001 7285 0.249826 AGTTCGCGGAAAAACGGGTA 60.250 50.000 6.13 0.00 45.53 3.69
6002 7286 0.585838 GTTCGCGGAAAAACGGGTAA 59.414 50.000 6.13 0.00 45.53 2.85
6003 7287 1.003008 GTTCGCGGAAAAACGGGTAAA 60.003 47.619 6.13 0.00 45.53 2.01
6004 7288 1.303309 TCGCGGAAAAACGGGTAAAA 58.697 45.000 6.13 0.00 45.53 1.52
6005 7289 1.672881 TCGCGGAAAAACGGGTAAAAA 59.327 42.857 6.13 0.00 45.53 1.94
6027 7311 8.947055 AAAAAGATATTTGCGGAATATGCTTT 57.053 26.923 9.18 12.82 40.26 3.51
6028 7312 8.947055 AAAAGATATTTGCGGAATATGCTTTT 57.053 26.923 19.87 19.87 40.26 2.27
6029 7313 8.947055 AAAGATATTTGCGGAATATGCTTTTT 57.053 26.923 9.18 3.99 40.26 1.94
6047 7331 2.500509 TTTACAAGTTGGCTTTGCGG 57.499 45.000 7.96 0.00 31.49 5.69
6048 7332 0.671251 TTACAAGTTGGCTTTGCGGG 59.329 50.000 7.96 0.00 31.49 6.13
6049 7333 1.175983 TACAAGTTGGCTTTGCGGGG 61.176 55.000 7.96 0.00 31.49 5.73
6050 7334 2.123468 AAGTTGGCTTTGCGGGGT 60.123 55.556 0.00 0.00 0.00 4.95
6051 7335 2.200337 AAGTTGGCTTTGCGGGGTC 61.200 57.895 0.00 0.00 0.00 4.46
6052 7336 2.597510 GTTGGCTTTGCGGGGTCT 60.598 61.111 0.00 0.00 0.00 3.85
6053 7337 2.597217 TTGGCTTTGCGGGGTCTG 60.597 61.111 0.00 0.00 0.00 3.51
6054 7338 4.659172 TGGCTTTGCGGGGTCTGG 62.659 66.667 0.00 0.00 0.00 3.86
6055 7339 4.660938 GGCTTTGCGGGGTCTGGT 62.661 66.667 0.00 0.00 0.00 4.00
6056 7340 3.056328 GCTTTGCGGGGTCTGGTC 61.056 66.667 0.00 0.00 0.00 4.02
6057 7341 2.750350 CTTTGCGGGGTCTGGTCT 59.250 61.111 0.00 0.00 0.00 3.85
6058 7342 1.672356 CTTTGCGGGGTCTGGTCTG 60.672 63.158 0.00 0.00 0.00 3.51
6059 7343 3.190738 TTTGCGGGGTCTGGTCTGG 62.191 63.158 0.00 0.00 0.00 3.86
6066 7350 4.008933 GTCTGGTCTGGCGCCACT 62.009 66.667 29.03 0.00 31.85 4.00
6067 7351 3.695606 TCTGGTCTGGCGCCACTC 61.696 66.667 29.03 20.72 31.85 3.51
6068 7352 4.767255 CTGGTCTGGCGCCACTCC 62.767 72.222 29.03 28.54 31.85 3.85
6070 7354 4.459089 GGTCTGGCGCCACTCCTC 62.459 72.222 29.03 13.56 0.00 3.71
6071 7355 4.459089 GTCTGGCGCCACTCCTCC 62.459 72.222 29.03 5.74 0.00 4.30
6079 7363 3.077556 CCACTCCTCCCGGTCCAG 61.078 72.222 0.00 0.00 0.00 3.86
6080 7364 2.037367 CACTCCTCCCGGTCCAGA 59.963 66.667 0.00 0.00 0.00 3.86
6081 7365 1.609501 CACTCCTCCCGGTCCAGAA 60.610 63.158 0.00 0.00 0.00 3.02
6082 7366 1.157751 ACTCCTCCCGGTCCAGAAA 59.842 57.895 0.00 0.00 0.00 2.52
6083 7367 0.473117 ACTCCTCCCGGTCCAGAAAA 60.473 55.000 0.00 0.00 0.00 2.29
6084 7368 0.036294 CTCCTCCCGGTCCAGAAAAC 60.036 60.000 0.00 0.00 0.00 2.43
6085 7369 1.002502 CCTCCCGGTCCAGAAAACC 60.003 63.158 0.00 0.00 0.00 3.27
6086 7370 1.489560 CCTCCCGGTCCAGAAAACCT 61.490 60.000 0.00 0.00 34.45 3.50
6087 7371 1.272807 CTCCCGGTCCAGAAAACCTA 58.727 55.000 0.00 0.00 34.45 3.08
6088 7372 1.626825 CTCCCGGTCCAGAAAACCTAA 59.373 52.381 0.00 0.00 34.45 2.69
6089 7373 2.039348 CTCCCGGTCCAGAAAACCTAAA 59.961 50.000 0.00 0.00 34.45 1.85
6090 7374 2.645797 TCCCGGTCCAGAAAACCTAAAT 59.354 45.455 0.00 0.00 34.45 1.40
6091 7375 3.074836 TCCCGGTCCAGAAAACCTAAATT 59.925 43.478 0.00 0.00 34.45 1.82
6092 7376 3.830178 CCCGGTCCAGAAAACCTAAATTT 59.170 43.478 0.00 0.00 34.45 1.82
6093 7377 5.011586 CCCGGTCCAGAAAACCTAAATTTA 58.988 41.667 0.00 0.00 34.45 1.40
6094 7378 5.106038 CCCGGTCCAGAAAACCTAAATTTAC 60.106 44.000 0.00 0.00 34.45 2.01
6095 7379 5.474189 CCGGTCCAGAAAACCTAAATTTACA 59.526 40.000 0.00 0.00 34.45 2.41
6096 7380 6.376177 CGGTCCAGAAAACCTAAATTTACAC 58.624 40.000 0.00 0.00 34.45 2.90
6097 7381 6.569035 CGGTCCAGAAAACCTAAATTTACACC 60.569 42.308 0.00 0.00 34.45 4.16
6098 7382 6.492429 GGTCCAGAAAACCTAAATTTACACCT 59.508 38.462 0.00 0.00 33.78 4.00
6099 7383 7.309012 GGTCCAGAAAACCTAAATTTACACCTC 60.309 40.741 0.00 0.00 33.78 3.85
6100 7384 7.229907 GTCCAGAAAACCTAAATTTACACCTCA 59.770 37.037 0.00 0.00 0.00 3.86
6101 7385 7.780745 TCCAGAAAACCTAAATTTACACCTCAA 59.219 33.333 0.00 0.00 0.00 3.02
6102 7386 8.585018 CCAGAAAACCTAAATTTACACCTCAAT 58.415 33.333 0.00 0.00 0.00 2.57
6103 7387 9.981114 CAGAAAACCTAAATTTACACCTCAATT 57.019 29.630 0.00 0.00 0.00 2.32
6109 7393 9.533831 ACCTAAATTTACACCTCAATTTGATCT 57.466 29.630 0.00 0.00 34.94 2.75
6115 7399 8.684386 TTTACACCTCAATTTGATCTAACACA 57.316 30.769 0.00 0.00 0.00 3.72
6116 7400 8.684386 TTACACCTCAATTTGATCTAACACAA 57.316 30.769 0.00 0.00 0.00 3.33
6117 7401 7.765695 ACACCTCAATTTGATCTAACACAAT 57.234 32.000 0.00 0.00 0.00 2.71
6118 7402 7.596494 ACACCTCAATTTGATCTAACACAATG 58.404 34.615 0.00 0.00 0.00 2.82
6119 7403 6.529125 CACCTCAATTTGATCTAACACAATGC 59.471 38.462 0.00 0.00 0.00 3.56
6120 7404 6.209192 ACCTCAATTTGATCTAACACAATGCA 59.791 34.615 0.00 0.00 0.00 3.96
6121 7405 7.093640 ACCTCAATTTGATCTAACACAATGCAT 60.094 33.333 0.00 0.00 0.00 3.96
6122 7406 7.762615 CCTCAATTTGATCTAACACAATGCATT 59.237 33.333 5.99 5.99 0.00 3.56
6123 7407 9.146984 CTCAATTTGATCTAACACAATGCATTT 57.853 29.630 9.83 0.00 0.00 2.32
6124 7408 9.142515 TCAATTTGATCTAACACAATGCATTTC 57.857 29.630 9.83 2.80 0.00 2.17
6125 7409 9.146984 CAATTTGATCTAACACAATGCATTTCT 57.853 29.630 9.83 0.00 0.00 2.52
6126 7410 9.715121 AATTTGATCTAACACAATGCATTTCTT 57.285 25.926 9.83 3.85 0.00 2.52
6127 7411 9.715121 ATTTGATCTAACACAATGCATTTCTTT 57.285 25.926 9.83 5.37 0.00 2.52
6128 7412 8.523523 TTGATCTAACACAATGCATTTCTTTG 57.476 30.769 9.83 7.32 36.31 2.77
6129 7413 6.587226 TGATCTAACACAATGCATTTCTTTGC 59.413 34.615 9.83 0.00 43.07 3.68
6130 7414 6.088016 TCTAACACAATGCATTTCTTTGCT 57.912 33.333 9.83 0.00 43.18 3.91
6131 7415 6.514947 TCTAACACAATGCATTTCTTTGCTT 58.485 32.000 9.83 5.14 43.18 3.91
6132 7416 6.985645 TCTAACACAATGCATTTCTTTGCTTT 59.014 30.769 9.83 0.00 43.18 3.51
6133 7417 6.439675 AACACAATGCATTTCTTTGCTTTT 57.560 29.167 9.83 0.00 43.18 2.27
6134 7418 6.439675 ACACAATGCATTTCTTTGCTTTTT 57.560 29.167 9.83 0.00 43.18 1.94
6135 7419 6.488817 ACACAATGCATTTCTTTGCTTTTTC 58.511 32.000 9.83 0.00 43.18 2.29
6136 7420 6.093771 ACACAATGCATTTCTTTGCTTTTTCA 59.906 30.769 9.83 0.00 43.18 2.69
6137 7421 6.967767 CACAATGCATTTCTTTGCTTTTTCAA 59.032 30.769 9.83 0.00 43.18 2.69
6138 7422 6.968335 ACAATGCATTTCTTTGCTTTTTCAAC 59.032 30.769 9.83 0.00 43.18 3.18
6139 7423 6.680874 ATGCATTTCTTTGCTTTTTCAACA 57.319 29.167 0.00 0.00 43.18 3.33
6140 7424 6.492007 TGCATTTCTTTGCTTTTTCAACAA 57.508 29.167 0.00 0.00 43.18 2.83
6141 7425 6.313252 TGCATTTCTTTGCTTTTTCAACAAC 58.687 32.000 0.00 0.00 43.18 3.32
6142 7426 6.072838 TGCATTTCTTTGCTTTTTCAACAACA 60.073 30.769 0.00 0.00 43.18 3.33
6143 7427 6.968335 GCATTTCTTTGCTTTTTCAACAACAT 59.032 30.769 0.00 0.00 39.57 2.71
6144 7428 7.485595 GCATTTCTTTGCTTTTTCAACAACATT 59.514 29.630 0.00 0.00 39.57 2.71
6145 7429 8.790674 CATTTCTTTGCTTTTTCAACAACATTG 58.209 29.630 0.00 0.00 0.00 2.82
6146 7430 6.419980 TCTTTGCTTTTTCAACAACATTGG 57.580 33.333 0.00 0.00 0.00 3.16
6147 7431 6.169094 TCTTTGCTTTTTCAACAACATTGGA 58.831 32.000 0.00 0.00 0.00 3.53
6148 7432 6.822676 TCTTTGCTTTTTCAACAACATTGGAT 59.177 30.769 0.00 0.00 0.00 3.41
6149 7433 7.984050 TCTTTGCTTTTTCAACAACATTGGATA 59.016 29.630 0.00 0.00 0.00 2.59
6150 7434 7.475771 TTGCTTTTTCAACAACATTGGATAC 57.524 32.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.169230 GATCTCGCGTCTGTCAGTGT 59.831 55.000 5.77 0.00 0.00 3.55
34 35 0.524392 GGATCTCGCGTCTGTCAGTG 60.524 60.000 5.77 0.00 0.00 3.66
35 36 0.960861 TGGATCTCGCGTCTGTCAGT 60.961 55.000 5.77 0.00 0.00 3.41
36 37 0.524392 GTGGATCTCGCGTCTGTCAG 60.524 60.000 5.77 0.00 0.00 3.51
37 38 1.506718 GTGGATCTCGCGTCTGTCA 59.493 57.895 5.77 0.00 0.00 3.58
46 47 1.433879 GGTCACCTCGTGGATCTCG 59.566 63.158 11.17 0.00 37.04 4.04
47 48 1.817209 GGGTCACCTCGTGGATCTC 59.183 63.158 11.17 0.00 37.04 2.75
54 55 3.907260 TAGTCGCGGGTCACCTCGT 62.907 63.158 6.13 0.00 44.96 4.18
55 56 2.001361 ATTAGTCGCGGGTCACCTCG 62.001 60.000 6.13 0.00 46.03 4.63
79 80 1.676014 GGGGTCACATCTTTCGTCAGG 60.676 57.143 0.00 0.00 0.00 3.86
115 119 3.365265 TCGCAGAGCAGCTGTCGA 61.365 61.111 16.64 13.20 46.62 4.20
180 184 3.550656 GCATGTAGCCGTATCGCC 58.449 61.111 0.00 0.00 37.23 5.54
212 216 1.845627 CTGCACCACATCTCCACCCT 61.846 60.000 0.00 0.00 0.00 4.34
215 219 0.674895 GGACTGCACCACATCTCCAC 60.675 60.000 0.00 0.00 0.00 4.02
218 222 1.078143 GGGGACTGCACCACATCTC 60.078 63.158 0.00 0.00 37.60 2.75
263 267 4.447290 TCCTCTGAATCTCTCGTAGACAG 58.553 47.826 0.00 0.00 36.93 3.51
300 304 0.645496 TCCTATCCCAGCACCCCTAA 59.355 55.000 0.00 0.00 0.00 2.69
302 306 0.695803 CTTCCTATCCCAGCACCCCT 60.696 60.000 0.00 0.00 0.00 4.79
336 342 2.499693 CCGCCCAGGAATTTAACCAATT 59.500 45.455 0.00 0.00 45.00 2.32
439 445 4.844085 TCAAGAGGTGACCCTTCTTCATTA 59.156 41.667 0.00 0.00 42.86 1.90
440 446 3.652869 TCAAGAGGTGACCCTTCTTCATT 59.347 43.478 0.00 0.00 42.86 2.57
457 858 2.628178 TCTCCTCGAGTTTGCTTCAAGA 59.372 45.455 12.31 0.00 0.00 3.02
462 863 3.181465 TGTTCTTCTCCTCGAGTTTGCTT 60.181 43.478 12.31 0.00 0.00 3.91
481 882 2.556189 TGTGCAGTGTGTTTCTTGTGTT 59.444 40.909 0.00 0.00 0.00 3.32
497 898 1.543607 CACATGGTGGGTATTGTGCA 58.456 50.000 0.00 0.00 33.78 4.57
528 929 5.866207 TCCCCTTTTCTCACTCTAGAAAAC 58.134 41.667 7.50 0.00 45.78 2.43
533 934 4.097418 TCCTTCCCCTTTTCTCACTCTAG 58.903 47.826 0.00 0.00 0.00 2.43
536 937 3.790089 TTCCTTCCCCTTTTCTCACTC 57.210 47.619 0.00 0.00 0.00 3.51
537 938 3.722101 TCTTTCCTTCCCCTTTTCTCACT 59.278 43.478 0.00 0.00 0.00 3.41
538 939 4.100279 TCTTTCCTTCCCCTTTTCTCAC 57.900 45.455 0.00 0.00 0.00 3.51
539 940 4.509122 CCATCTTTCCTTCCCCTTTTCTCA 60.509 45.833 0.00 0.00 0.00 3.27
540 941 4.019858 CCATCTTTCCTTCCCCTTTTCTC 58.980 47.826 0.00 0.00 0.00 2.87
541 942 3.662642 TCCATCTTTCCTTCCCCTTTTCT 59.337 43.478 0.00 0.00 0.00 2.52
542 943 3.764434 GTCCATCTTTCCTTCCCCTTTTC 59.236 47.826 0.00 0.00 0.00 2.29
562 963 2.332063 ATGAATGATGGTGTCCCGTC 57.668 50.000 0.00 0.00 45.61 4.79
563 964 2.026356 TGAATGAATGATGGTGTCCCGT 60.026 45.455 0.00 0.00 0.00 5.28
566 967 7.338800 AGTTAATGAATGAATGATGGTGTCC 57.661 36.000 0.00 0.00 0.00 4.02
682 1083 8.734386 CCAGATTTAATGGTAGATATTGCCTTC 58.266 37.037 0.00 0.00 32.85 3.46
716 1279 9.624373 ACTTCTGCTAATCTCATGTTCATATTT 57.376 29.630 0.00 0.00 0.00 1.40
718 1281 9.053840 CAACTTCTGCTAATCTCATGTTCATAT 57.946 33.333 0.00 0.00 0.00 1.78
719 1282 8.260114 TCAACTTCTGCTAATCTCATGTTCATA 58.740 33.333 0.00 0.00 0.00 2.15
720 1283 7.108194 TCAACTTCTGCTAATCTCATGTTCAT 58.892 34.615 0.00 0.00 0.00 2.57
721 1284 6.466812 TCAACTTCTGCTAATCTCATGTTCA 58.533 36.000 0.00 0.00 0.00 3.18
722 1285 6.815641 TCTCAACTTCTGCTAATCTCATGTTC 59.184 38.462 0.00 0.00 0.00 3.18
723 1286 6.705302 TCTCAACTTCTGCTAATCTCATGTT 58.295 36.000 0.00 0.00 0.00 2.71
724 1287 6.291648 TCTCAACTTCTGCTAATCTCATGT 57.708 37.500 0.00 0.00 0.00 3.21
725 1288 6.036953 GGTTCTCAACTTCTGCTAATCTCATG 59.963 42.308 0.00 0.00 0.00 3.07
726 1289 6.070309 AGGTTCTCAACTTCTGCTAATCTCAT 60.070 38.462 0.00 0.00 0.00 2.90
727 1290 5.247110 AGGTTCTCAACTTCTGCTAATCTCA 59.753 40.000 0.00 0.00 0.00 3.27
928 1492 3.393970 CTCGCCCTCCCTGCTTCA 61.394 66.667 0.00 0.00 0.00 3.02
984 1548 2.066393 CATCTCGGCTCCTTCCCCA 61.066 63.158 0.00 0.00 0.00 4.96
1177 1741 0.807667 CCAGACCGCTTCCAATCGAG 60.808 60.000 0.00 0.00 0.00 4.04
1289 1853 2.825836 GCCTTCCCGCACATCAGG 60.826 66.667 0.00 0.00 0.00 3.86
1371 1935 3.113043 ACGAAACCCTAGAGCCCTAATT 58.887 45.455 0.00 0.00 0.00 1.40
1493 2057 8.518430 AAGCACAACCAATGAATATACACATA 57.482 30.769 0.00 0.00 0.00 2.29
1649 2213 0.257328 TTGTCTTTGGGCAGTCACCA 59.743 50.000 0.00 0.00 35.88 4.17
1816 2380 5.345741 CCGTTTTTGAAACATAGGCATCAAG 59.654 40.000 4.65 0.00 33.71 3.02
2275 2842 6.714810 AGTATTGATTTTGTCTTACCACAGCA 59.285 34.615 0.00 0.00 0.00 4.41
2280 2847 8.726988 GCAGTTAGTATTGATTTTGTCTTACCA 58.273 33.333 0.00 0.00 0.00 3.25
2302 2869 1.595093 GCATTTTACGGGGCAGCAGT 61.595 55.000 0.00 0.00 0.00 4.40
2360 2938 6.067217 ACTAAGCAGTTCAATCACCCTATT 57.933 37.500 0.00 0.00 0.00 1.73
2361 2939 5.700402 ACTAAGCAGTTCAATCACCCTAT 57.300 39.130 0.00 0.00 0.00 2.57
2363 2941 4.777896 TCTACTAAGCAGTTCAATCACCCT 59.222 41.667 0.00 0.00 36.14 4.34
2364 2942 4.870991 GTCTACTAAGCAGTTCAATCACCC 59.129 45.833 0.00 0.00 36.14 4.61
2365 2943 5.479306 TGTCTACTAAGCAGTTCAATCACC 58.521 41.667 0.00 0.00 36.14 4.02
2366 2944 7.602517 ATTGTCTACTAAGCAGTTCAATCAC 57.397 36.000 0.00 0.00 36.14 3.06
2367 2945 7.877612 TCAATTGTCTACTAAGCAGTTCAATCA 59.122 33.333 5.13 0.00 36.14 2.57
2368 2946 8.256611 TCAATTGTCTACTAAGCAGTTCAATC 57.743 34.615 5.13 0.00 36.14 2.67
2370 2948 6.650807 CCTCAATTGTCTACTAAGCAGTTCAA 59.349 38.462 5.13 0.00 36.14 2.69
2402 2999 6.959639 AACTAGCTTCAAAATCAACTTCCA 57.040 33.333 0.00 0.00 0.00 3.53
2654 3275 5.980715 GCTCCTTCTACAAGACTTGCTATAC 59.019 44.000 15.24 0.00 0.00 1.47
3362 3985 1.963515 AGGTGGCCTTTTTACAGCAAG 59.036 47.619 3.32 0.00 35.24 4.01
3441 4064 5.359576 AGCATGCAGAATTCCCGTATTTTAA 59.640 36.000 21.98 0.00 0.00 1.52
3601 4224 7.848128 TGATAGTAAAGGTTAGGACAGGAAAG 58.152 38.462 0.00 0.00 0.00 2.62
3922 4579 9.454859 GCCTCATAGCATTACCTTAAATAGATT 57.545 33.333 0.00 0.00 0.00 2.40
3923 4580 8.830741 AGCCTCATAGCATTACCTTAAATAGAT 58.169 33.333 0.00 0.00 34.23 1.98
3924 4581 8.097038 CAGCCTCATAGCATTACCTTAAATAGA 58.903 37.037 0.00 0.00 34.23 1.98
3925 4582 7.148340 GCAGCCTCATAGCATTACCTTAAATAG 60.148 40.741 0.00 0.00 34.23 1.73
3926 4583 6.655003 GCAGCCTCATAGCATTACCTTAAATA 59.345 38.462 0.00 0.00 34.23 1.40
3927 4584 5.474876 GCAGCCTCATAGCATTACCTTAAAT 59.525 40.000 0.00 0.00 34.23 1.40
3928 4585 4.821805 GCAGCCTCATAGCATTACCTTAAA 59.178 41.667 0.00 0.00 34.23 1.52
3929 4586 4.103153 AGCAGCCTCATAGCATTACCTTAA 59.897 41.667 0.00 0.00 34.23 1.85
3930 4587 3.648067 AGCAGCCTCATAGCATTACCTTA 59.352 43.478 0.00 0.00 34.23 2.69
3931 4588 2.441001 AGCAGCCTCATAGCATTACCTT 59.559 45.455 0.00 0.00 34.23 3.50
3932 4589 2.053244 AGCAGCCTCATAGCATTACCT 58.947 47.619 0.00 0.00 34.23 3.08
4303 5563 6.018262 TGTTTGAGTGGTTAAATGAAGAGACG 60.018 38.462 0.00 0.00 0.00 4.18
4483 5743 7.840342 ACAGCTAAACTCTACAGAATTCATG 57.160 36.000 8.44 5.85 0.00 3.07
4647 5907 6.513806 AATTACATACAAAGCAGCATCACA 57.486 33.333 0.00 0.00 0.00 3.58
4806 6066 6.900568 TCCAAACAATTGCAGTAAGTTTTG 57.099 33.333 5.05 6.18 35.10 2.44
4890 6156 4.443725 CAGAGATCACAGCACGCTAATAAG 59.556 45.833 0.00 0.00 0.00 1.73
5107 6373 4.012374 CAGACAAATTAGATGCCAGGTGT 58.988 43.478 0.00 0.00 0.00 4.16
5223 6489 1.337167 GGTGCTCAAGGGCATGAAAAC 60.337 52.381 0.00 0.00 44.34 2.43
5583 6850 2.204461 AGCTGCCTGCAATGCAACA 61.204 52.632 9.92 9.82 45.94 3.33
5690 6971 3.880490 ACTTCCACAGCAATCGTAAAACA 59.120 39.130 0.00 0.00 0.00 2.83
5697 6978 1.800805 AGACACTTCCACAGCAATCG 58.199 50.000 0.00 0.00 0.00 3.34
5717 7001 5.518847 CGCAAAAGAACCAATCTCGACTATA 59.481 40.000 0.00 0.00 37.42 1.31
5718 7002 4.330074 CGCAAAAGAACCAATCTCGACTAT 59.670 41.667 0.00 0.00 37.42 2.12
5756 7040 1.747774 CCTGGGCAAAACCACAAGG 59.252 57.895 0.00 0.00 42.05 3.61
5786 7070 2.202987 GCGAGATGCACCTGGGAG 60.203 66.667 0.00 0.00 45.45 4.30
5807 7091 2.047844 TGGACGAGAAGCTGCTGC 60.048 61.111 0.00 7.62 40.05 5.25
5809 7093 0.459489 GATCTGGACGAGAAGCTGCT 59.541 55.000 0.00 0.00 33.12 4.24
5810 7094 0.174389 TGATCTGGACGAGAAGCTGC 59.826 55.000 0.00 0.00 33.12 5.25
5812 7096 3.529533 CAAATGATCTGGACGAGAAGCT 58.470 45.455 0.00 0.00 33.12 3.74
5813 7097 2.031437 GCAAATGATCTGGACGAGAAGC 59.969 50.000 0.00 0.00 33.12 3.86
5864 7148 3.496160 GGTTGGTCTACTTCTCCTTTGCA 60.496 47.826 0.00 0.00 0.00 4.08
5874 7158 2.949644 GTGTTTGCTGGTTGGTCTACTT 59.050 45.455 0.00 0.00 0.00 2.24
5933 7217 1.412079 CAGGGTCTGCTAGAGATGCT 58.588 55.000 0.00 0.00 31.63 3.79
5934 7218 3.984838 CAGGGTCTGCTAGAGATGC 57.015 57.895 0.00 0.00 31.63 3.91
5968 7252 0.223513 CGAACTGCAAACGCGTTTTG 59.776 50.000 33.05 26.38 46.57 2.44
5969 7253 1.468340 GCGAACTGCAAACGCGTTTT 61.468 50.000 33.05 19.44 45.45 2.43
5970 7254 1.937362 GCGAACTGCAAACGCGTTT 60.937 52.632 30.36 30.36 45.45 3.60
5971 7255 2.351888 GCGAACTGCAAACGCGTT 60.352 55.556 20.79 20.79 45.45 4.84
5974 7258 2.975167 TTTCCGCGAACTGCAAACGC 62.975 55.000 8.23 17.60 46.97 4.84
5975 7259 0.590230 TTTTCCGCGAACTGCAAACG 60.590 50.000 8.23 0.00 46.97 3.60
5976 7260 1.254313 GTTTTTCCGCGAACTGCAAAC 59.746 47.619 8.23 4.18 46.97 2.93
5977 7261 1.551145 GTTTTTCCGCGAACTGCAAA 58.449 45.000 8.23 0.00 46.97 3.68
5978 7262 0.590230 CGTTTTTCCGCGAACTGCAA 60.590 50.000 8.23 0.00 46.97 4.08
5979 7263 1.010574 CGTTTTTCCGCGAACTGCA 60.011 52.632 8.23 0.00 46.97 4.41
5980 7264 1.724581 CCGTTTTTCCGCGAACTGC 60.725 57.895 8.23 0.00 41.47 4.40
5981 7265 1.082366 CCCGTTTTTCCGCGAACTG 60.082 57.895 8.23 0.00 0.00 3.16
5982 7266 0.249826 TACCCGTTTTTCCGCGAACT 60.250 50.000 8.23 0.00 0.00 3.01
5983 7267 0.585838 TTACCCGTTTTTCCGCGAAC 59.414 50.000 8.23 2.38 0.00 3.95
5984 7268 1.303309 TTTACCCGTTTTTCCGCGAA 58.697 45.000 8.23 0.00 0.00 4.70
5985 7269 1.303309 TTTTACCCGTTTTTCCGCGA 58.697 45.000 8.23 0.00 0.00 5.87
5986 7270 2.116787 TTTTTACCCGTTTTTCCGCG 57.883 45.000 0.00 0.00 0.00 6.46
6002 7286 8.947055 AAAGCATATTCCGCAAATATCTTTTT 57.053 26.923 13.37 7.43 38.28 1.94
6003 7287 8.947055 AAAAGCATATTCCGCAAATATCTTTT 57.053 26.923 18.47 18.47 38.28 2.27
6004 7288 8.947055 AAAAAGCATATTCCGCAAATATCTTT 57.053 26.923 13.37 13.37 38.28 2.52
6026 7310 3.190874 CCGCAAAGCCAACTTGTAAAAA 58.809 40.909 0.00 0.00 35.85 1.94
6027 7311 2.482142 CCCGCAAAGCCAACTTGTAAAA 60.482 45.455 0.00 0.00 35.85 1.52
6028 7312 1.067821 CCCGCAAAGCCAACTTGTAAA 59.932 47.619 0.00 0.00 35.85 2.01
6029 7313 0.671251 CCCGCAAAGCCAACTTGTAA 59.329 50.000 0.00 0.00 35.85 2.41
6030 7314 1.175983 CCCCGCAAAGCCAACTTGTA 61.176 55.000 0.00 0.00 35.85 2.41
6031 7315 2.498056 CCCCGCAAAGCCAACTTGT 61.498 57.895 0.00 0.00 35.85 3.16
6032 7316 2.339712 CCCCGCAAAGCCAACTTG 59.660 61.111 0.00 0.00 35.85 3.16
6033 7317 2.123468 ACCCCGCAAAGCCAACTT 60.123 55.556 0.00 0.00 37.90 2.66
6034 7318 2.597510 GACCCCGCAAAGCCAACT 60.598 61.111 0.00 0.00 0.00 3.16
6035 7319 2.597510 AGACCCCGCAAAGCCAAC 60.598 61.111 0.00 0.00 0.00 3.77
6036 7320 2.597217 CAGACCCCGCAAAGCCAA 60.597 61.111 0.00 0.00 0.00 4.52
6037 7321 4.659172 CCAGACCCCGCAAAGCCA 62.659 66.667 0.00 0.00 0.00 4.75
6038 7322 4.660938 ACCAGACCCCGCAAAGCC 62.661 66.667 0.00 0.00 0.00 4.35
6039 7323 3.056328 GACCAGACCCCGCAAAGC 61.056 66.667 0.00 0.00 0.00 3.51
6040 7324 1.672356 CAGACCAGACCCCGCAAAG 60.672 63.158 0.00 0.00 0.00 2.77
6041 7325 2.429930 CAGACCAGACCCCGCAAA 59.570 61.111 0.00 0.00 0.00 3.68
6042 7326 3.636231 CCAGACCAGACCCCGCAA 61.636 66.667 0.00 0.00 0.00 4.85
6049 7333 3.941657 GAGTGGCGCCAGACCAGAC 62.942 68.421 33.73 16.87 38.04 3.51
6050 7334 3.695606 GAGTGGCGCCAGACCAGA 61.696 66.667 33.73 1.60 38.04 3.86
6051 7335 4.767255 GGAGTGGCGCCAGACCAG 62.767 72.222 33.39 0.00 38.04 4.00
6053 7337 4.459089 GAGGAGTGGCGCCAGACC 62.459 72.222 33.73 32.75 0.00 3.85
6054 7338 4.459089 GGAGGAGTGGCGCCAGAC 62.459 72.222 33.73 25.63 0.00 3.51
6068 7352 1.272807 TAGGTTTTCTGGACCGGGAG 58.727 55.000 6.32 0.00 42.11 4.30
6069 7353 1.732117 TTAGGTTTTCTGGACCGGGA 58.268 50.000 6.32 0.00 42.11 5.14
6070 7354 2.572209 TTTAGGTTTTCTGGACCGGG 57.428 50.000 6.32 0.00 42.11 5.73
6071 7355 5.474189 TGTAAATTTAGGTTTTCTGGACCGG 59.526 40.000 0.00 0.00 42.11 5.28
6072 7356 6.376177 GTGTAAATTTAGGTTTTCTGGACCG 58.624 40.000 0.00 0.00 42.11 4.79
6073 7357 6.492429 AGGTGTAAATTTAGGTTTTCTGGACC 59.508 38.462 0.00 0.00 37.44 4.46
6074 7358 7.229907 TGAGGTGTAAATTTAGGTTTTCTGGAC 59.770 37.037 0.00 0.00 0.00 4.02
6075 7359 7.291566 TGAGGTGTAAATTTAGGTTTTCTGGA 58.708 34.615 0.00 0.00 0.00 3.86
6076 7360 7.519032 TGAGGTGTAAATTTAGGTTTTCTGG 57.481 36.000 0.00 0.00 0.00 3.86
6077 7361 9.981114 AATTGAGGTGTAAATTTAGGTTTTCTG 57.019 29.630 0.00 0.00 0.00 3.02
6083 7367 9.533831 AGATCAAATTGAGGTGTAAATTTAGGT 57.466 29.630 1.10 0.00 34.92 3.08
6089 7373 9.295825 TGTGTTAGATCAAATTGAGGTGTAAAT 57.704 29.630 1.10 0.00 0.00 1.40
6090 7374 8.684386 TGTGTTAGATCAAATTGAGGTGTAAA 57.316 30.769 1.10 0.00 0.00 2.01
6091 7375 8.684386 TTGTGTTAGATCAAATTGAGGTGTAA 57.316 30.769 1.10 0.00 0.00 2.41
6092 7376 8.729756 CATTGTGTTAGATCAAATTGAGGTGTA 58.270 33.333 1.10 0.00 0.00 2.90
6093 7377 7.596494 CATTGTGTTAGATCAAATTGAGGTGT 58.404 34.615 1.10 0.00 0.00 4.16
6094 7378 6.529125 GCATTGTGTTAGATCAAATTGAGGTG 59.471 38.462 1.10 0.00 0.00 4.00
6095 7379 6.209192 TGCATTGTGTTAGATCAAATTGAGGT 59.791 34.615 1.10 0.00 0.00 3.85
6096 7380 6.623486 TGCATTGTGTTAGATCAAATTGAGG 58.377 36.000 1.10 0.00 0.00 3.86
6097 7381 8.697846 AATGCATTGTGTTAGATCAAATTGAG 57.302 30.769 12.09 0.00 0.00 3.02
6098 7382 9.142515 GAAATGCATTGTGTTAGATCAAATTGA 57.857 29.630 13.82 0.00 0.00 2.57
6099 7383 9.146984 AGAAATGCATTGTGTTAGATCAAATTG 57.853 29.630 13.82 0.00 0.00 2.32
6100 7384 9.715121 AAGAAATGCATTGTGTTAGATCAAATT 57.285 25.926 13.82 0.00 0.00 1.82
6101 7385 9.715121 AAAGAAATGCATTGTGTTAGATCAAAT 57.285 25.926 13.82 0.00 0.00 2.32
6102 7386 8.980610 CAAAGAAATGCATTGTGTTAGATCAAA 58.019 29.630 13.82 0.00 0.00 2.69
6103 7387 7.116662 GCAAAGAAATGCATTGTGTTAGATCAA 59.883 33.333 13.82 0.00 45.70 2.57
6104 7388 6.587226 GCAAAGAAATGCATTGTGTTAGATCA 59.413 34.615 13.82 0.00 45.70 2.92
6105 7389 6.986118 GCAAAGAAATGCATTGTGTTAGATC 58.014 36.000 13.82 4.00 45.70 2.75
6106 7390 6.956299 GCAAAGAAATGCATTGTGTTAGAT 57.044 33.333 13.82 0.00 45.70 1.98
6118 7402 6.313252 TGTTGTTGAAAAAGCAAAGAAATGC 58.687 32.000 0.00 0.00 46.78 3.56
6119 7403 8.790674 CAATGTTGTTGAAAAAGCAAAGAAATG 58.209 29.630 0.00 0.00 0.00 2.32
6120 7404 7.969508 CCAATGTTGTTGAAAAAGCAAAGAAAT 59.030 29.630 0.00 0.00 0.00 2.17
6121 7405 7.173907 TCCAATGTTGTTGAAAAAGCAAAGAAA 59.826 29.630 0.00 0.00 0.00 2.52
6122 7406 6.652481 TCCAATGTTGTTGAAAAAGCAAAGAA 59.348 30.769 0.00 0.00 0.00 2.52
6123 7407 6.169094 TCCAATGTTGTTGAAAAAGCAAAGA 58.831 32.000 0.00 0.00 0.00 2.52
6124 7408 6.419980 TCCAATGTTGTTGAAAAAGCAAAG 57.580 33.333 0.00 0.00 0.00 2.77
6125 7409 6.998968 ATCCAATGTTGTTGAAAAAGCAAA 57.001 29.167 0.00 0.00 0.00 3.68
6126 7410 7.044181 TGTATCCAATGTTGTTGAAAAAGCAA 58.956 30.769 0.00 0.00 0.00 3.91
6127 7411 6.577103 TGTATCCAATGTTGTTGAAAAAGCA 58.423 32.000 0.00 0.00 0.00 3.91
6128 7412 7.656707 ATGTATCCAATGTTGTTGAAAAAGC 57.343 32.000 0.00 0.00 0.00 3.51
6131 7415 9.906660 GTCTTATGTATCCAATGTTGTTGAAAA 57.093 29.630 0.00 0.00 0.00 2.29
6132 7416 9.072375 TGTCTTATGTATCCAATGTTGTTGAAA 57.928 29.630 0.00 0.00 0.00 2.69
6133 7417 8.628630 TGTCTTATGTATCCAATGTTGTTGAA 57.371 30.769 0.00 0.00 0.00 2.69
6134 7418 8.806429 ATGTCTTATGTATCCAATGTTGTTGA 57.194 30.769 0.00 0.00 0.00 3.18
6135 7419 8.676401 TGATGTCTTATGTATCCAATGTTGTTG 58.324 33.333 0.00 0.00 0.00 3.33
6136 7420 8.806429 TGATGTCTTATGTATCCAATGTTGTT 57.194 30.769 0.00 0.00 0.00 2.83
6137 7421 8.985315 ATGATGTCTTATGTATCCAATGTTGT 57.015 30.769 0.00 0.00 0.00 3.32
6138 7422 9.059260 TGATGATGTCTTATGTATCCAATGTTG 57.941 33.333 0.00 0.00 0.00 3.33
6139 7423 9.631257 TTGATGATGTCTTATGTATCCAATGTT 57.369 29.630 0.00 0.00 0.00 2.71
6140 7424 9.631257 TTTGATGATGTCTTATGTATCCAATGT 57.369 29.630 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.