Multiple sequence alignment - TraesCS4D01G281300

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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 TraesCS4D01G281300 chr4D 100.000 7302 0 0 1 7302 452547673 452554974 0.000000e+00 13485.0
1 TraesCS4D01G281300 chr4D 78.602 1388 191 48 461 1789 452312558 452313898 0.000000e+00 821.0
2 TraesCS4D01G281300 chr4D 79.550 1110 155 40 2283 3371 452314024 452315082 0.000000e+00 726.0
3 TraesCS4D01G281300 chr4D 78.711 512 86 8 1181 1682 452384531 452385029 3.290000e-83 320.0
4 TraesCS4D01G281300 chr4D 78.500 400 67 12 6418 6804 452391924 452392317 2.030000e-60 244.0
5 TraesCS4D01G281300 chr4D 76.098 410 72 16 6418 6806 452316298 452316702 2.690000e-44 191.0
6 TraesCS4D01G281300 chr4D 81.340 209 37 2 3144 3352 452390554 452390760 1.260000e-37 169.0
7 TraesCS4D01G281300 chr4D 78.800 250 48 5 1930 2179 294346212 294346456 5.860000e-36 163.0
8 TraesCS4D01G281300 chr4A 95.917 3968 136 16 336 4283 14359101 14355140 0.000000e+00 6407.0
9 TraesCS4D01G281300 chr4A 95.122 861 25 7 6080 6923 14354394 14353534 0.000000e+00 1341.0
10 TraesCS4D01G281300 chr4A 96.439 702 20 4 4277 4973 14355106 14354405 0.000000e+00 1153.0
11 TraesCS4D01G281300 chr4A 77.723 404 65 15 6421 6804 14757518 14757120 2.650000e-54 224.0
12 TraesCS4D01G281300 chr4A 80.323 310 45 10 1181 1477 14743939 14743633 3.430000e-53 220.0
13 TraesCS4D01G281300 chr4A 97.468 79 2 0 7032 7110 14353279 14353201 1.280000e-27 135.0
14 TraesCS4D01G281300 chr4A 93.443 61 3 1 201 260 14359179 14359119 1.010000e-13 89.8
15 TraesCS4D01G281300 chr4A 92.593 54 4 0 3 56 14359401 14359348 2.180000e-10 78.7
16 TraesCS4D01G281300 chr4A 83.333 84 13 1 3269 3352 14732918 14732836 7.860000e-10 76.8
17 TraesCS4D01G281300 chr4B 94.129 3526 141 20 336 3851 565733544 565737013 0.000000e+00 5304.0
18 TraesCS4D01G281300 chr4B 89.864 957 49 14 4291 5221 565737685 565738619 0.000000e+00 1186.0
19 TraesCS4D01G281300 chr4B 90.114 880 52 7 5221 6066 565738659 565739537 0.000000e+00 1110.0
20 TraesCS4D01G281300 chr4B 78.443 1387 196 52 461 1790 565526975 565528315 0.000000e+00 809.0
21 TraesCS4D01G281300 chr4B 79.982 1119 150 39 2283 3371 565528439 565529513 0.000000e+00 758.0
22 TraesCS4D01G281300 chr4B 96.092 435 16 1 3850 4283 565737175 565737609 0.000000e+00 708.0
23 TraesCS4D01G281300 chr4B 94.954 436 13 3 6479 6906 565739880 565740314 0.000000e+00 675.0
24 TraesCS4D01G281300 chr4B 80.531 791 123 23 394 1174 565602428 565603197 4.910000e-161 579.0
25 TraesCS4D01G281300 chr4B 92.935 368 22 1 6080 6443 565739512 565739879 3.880000e-147 532.0
26 TraesCS4D01G281300 chr4B 81.778 450 70 8 461 900 565525326 565525773 4.160000e-97 366.0
27 TraesCS4D01G281300 chr4B 78.711 512 86 13 1181 1682 565603243 565603741 3.290000e-83 320.0
28 TraesCS4D01G281300 chr4B 78.378 259 51 5 1930 2188 362143973 362144226 5.860000e-36 163.0
29 TraesCS4D01G281300 chr4B 97.674 86 2 0 7215 7300 565740818 565740903 1.640000e-31 148.0
30 TraesCS4D01G281300 chr4B 87.500 80 7 3 4624 4702 565529845 565529922 1.010000e-13 89.8
31 TraesCS4D01G281300 chr4B 95.918 49 2 0 210 258 565733476 565733524 6.070000e-11 80.5
32 TraesCS4D01G281300 chr4B 95.455 44 1 1 4277 4319 565737643 565737686 1.310000e-07 69.4
33 TraesCS4D01G281300 chr4B 100.000 34 0 0 288 321 565733525 565733558 6.120000e-06 63.9
34 TraesCS4D01G281300 chr2B 87.209 602 62 14 3381 3979 112468455 112467866 0.000000e+00 671.0
35 TraesCS4D01G281300 chr2A 89.684 475 34 13 3381 3845 270466389 270466858 6.310000e-165 592.0
36 TraesCS4D01G281300 chr2A 79.227 207 38 2 1987 2193 236837508 236837307 9.880000e-29 139.0
37 TraesCS4D01G281300 chr5A 84.817 573 63 14 3411 3971 343049754 343050314 8.280000e-154 555.0
38 TraesCS4D01G281300 chr2D 86.567 469 32 10 3381 3845 238157758 238158199 8.510000e-134 488.0
39 TraesCS4D01G281300 chr2D 92.000 250 17 2 3382 3630 426424636 426424883 1.510000e-91 348.0
40 TraesCS4D01G281300 chr2D 79.227 207 38 2 1987 2193 255618781 255618982 9.880000e-29 139.0
41 TraesCS4D01G281300 chr2D 97.436 39 0 1 4715 4752 605464080 605464042 1.700000e-06 65.8
42 TraesCS4D01G281300 chr2D 97.436 39 0 1 4715 4752 605579041 605579003 1.700000e-06 65.8
43 TraesCS4D01G281300 chr1B 82.017 595 66 28 3406 3988 656376618 656376053 1.110000e-127 468.0
44 TraesCS4D01G281300 chr1B 85.802 162 22 1 2040 2200 632656459 632656298 3.500000e-38 171.0
45 TraesCS4D01G281300 chr1B 90.411 73 7 0 2309 2381 544131788 544131860 6.030000e-16 97.1
46 TraesCS4D01G281300 chr1D 85.501 469 36 22 3382 3845 162063005 162062564 1.860000e-125 460.0
47 TraesCS4D01G281300 chr1D 78.547 289 52 9 4718 4999 463161514 463161799 1.620000e-41 182.0
48 TraesCS4D01G281300 chr6D 86.111 432 29 16 3560 3986 269699148 269699553 3.130000e-118 436.0
49 TraesCS4D01G281300 chr6D 79.310 203 40 2 1987 2188 310399726 310399525 2.750000e-29 141.0
50 TraesCS4D01G281300 chr3D 77.125 800 149 19 384 1173 13330274 13331049 4.050000e-117 433.0
51 TraesCS4D01G281300 chr7A 85.092 436 46 13 3382 3814 240725561 240725980 1.880000e-115 427.0
52 TraesCS4D01G281300 chr6B 85.648 432 32 14 3560 3986 422318808 422319214 1.880000e-115 427.0
53 TraesCS4D01G281300 chr7B 91.968 249 19 1 3382 3630 199754060 199754307 1.510000e-91 348.0
54 TraesCS4D01G281300 chr7B 92.373 118 9 0 3862 3979 199757874 199757991 1.260000e-37 169.0
55 TraesCS4D01G281300 chr3A 75.353 779 159 22 402 1172 23695861 23695108 1.950000e-90 344.0
56 TraesCS4D01G281300 chr3A 79.535 215 38 2 558 772 23771580 23771372 1.640000e-31 148.0
57 TraesCS4D01G281300 chr6A 86.280 328 27 9 3664 3986 383962184 383962498 2.520000e-89 340.0
58 TraesCS4D01G281300 chr3B 78.316 392 64 16 4715 5089 214568729 214568342 4.400000e-57 233.0
59 TraesCS4D01G281300 chr3B 75.000 468 101 8 706 1172 19381622 19382074 1.240000e-47 202.0
60 TraesCS4D01G281300 chr5D 77.411 394 65 20 4719 5094 310022144 310022531 5.740000e-51 213.0
61 TraesCS4D01G281300 chr5D 77.500 280 41 19 4719 4997 139455396 139455138 1.640000e-31 148.0
62 TraesCS4D01G281300 chr1A 91.473 129 11 0 3862 3990 222350487 222350615 2.090000e-40 178.0
63 TraesCS4D01G281300 chr5B 78.788 264 48 5 1938 2193 485912332 485912069 3.500000e-38 171.0
64 TraesCS4D01G281300 chr7D 80.085 236 35 7 4859 5094 287911043 287910820 1.630000e-36 165.0
65 TraesCS4D01G281300 chr7D 81.910 199 33 3 4826 5022 603659583 603659780 1.630000e-36 165.0
66 TraesCS4D01G281300 chr7D 83.721 172 26 2 4813 4982 40848730 40848559 2.110000e-35 161.0
67 TraesCS4D01G281300 chr7D 80.402 199 26 4 3798 3991 326053010 326052820 9.880000e-29 139.0


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 TraesCS4D01G281300 chr4D 452547673 452554974 7301 False 13485.000000 13485 100.000000 1 7302 1 chr4D.!!$F3 7301
1 TraesCS4D01G281300 chr4D 452312558 452316702 4144 False 579.333333 821 78.083333 461 6806 3 chr4D.!!$F4 6345
2 TraesCS4D01G281300 chr4D 452390554 452392317 1763 False 206.500000 244 79.920000 3144 6804 2 chr4D.!!$F5 3660
3 TraesCS4D01G281300 chr4A 14353201 14359401 6200 True 1534.083333 6407 95.163667 3 7110 6 chr4A.!!$R4 7107
4 TraesCS4D01G281300 chr4B 565733476 565740903 7427 False 987.680000 5304 94.713500 210 7300 10 chr4B.!!$F4 7090
5 TraesCS4D01G281300 chr4B 565525326 565529922 4596 False 505.700000 809 81.925750 461 4702 4 chr4B.!!$F2 4241
6 TraesCS4D01G281300 chr4B 565602428 565603741 1313 False 449.500000 579 79.621000 394 1682 2 chr4B.!!$F3 1288
7 TraesCS4D01G281300 chr2B 112467866 112468455 589 True 671.000000 671 87.209000 3381 3979 1 chr2B.!!$R1 598
8 TraesCS4D01G281300 chr5A 343049754 343050314 560 False 555.000000 555 84.817000 3411 3971 1 chr5A.!!$F1 560
9 TraesCS4D01G281300 chr1B 656376053 656376618 565 True 468.000000 468 82.017000 3406 3988 1 chr1B.!!$R2 582
10 TraesCS4D01G281300 chr3D 13330274 13331049 775 False 433.000000 433 77.125000 384 1173 1 chr3D.!!$F1 789
11 TraesCS4D01G281300 chr7B 199754060 199757991 3931 False 258.500000 348 92.170500 3382 3979 2 chr7B.!!$F1 597
12 TraesCS4D01G281300 chr3A 23695108 23695861 753 True 344.000000 344 75.353000 402 1172 1 chr3A.!!$R1 770

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
286 384 0.250295 TTTGGTCGTCCAGCAAGAGG 60.250 55.000 0.74 0.00 43.36 3.69 F
382 481 0.670854 GTCCACTCGCTCCCTGTTTC 60.671 60.000 0.00 0.00 0.00 2.78 F
1143 2909 1.749638 CGAGGCTACCGAGTGGAGT 60.750 63.158 0.00 0.00 39.21 3.85 F
1903 3740 1.871080 ATATTGCTGCAGCGGTAGAC 58.129 50.000 32.11 6.25 45.83 2.59 F
2220 4057 3.405831 TGACTCTGGAAACTCAGCAATG 58.594 45.455 0.00 0.00 34.91 2.82 F
3790 5716 1.277557 GCTGTTGTGATCCTCCTCTGT 59.722 52.381 0.00 0.00 0.00 3.41 F
5026 10883 0.532862 AGTTGACAAGTGGACGGCAG 60.533 55.000 0.00 0.00 0.00 4.85 F
5647 11546 0.465097 ATCTCCGAAGCTGCAATGGG 60.465 55.000 1.02 1.03 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 3008 0.593773 CTTTGTTTCCCACAACCGCG 60.594 55.000 0.00 0.0 45.54 6.46 R
1437 3257 0.790207 GCGATGTTTGAAGCTCGACA 59.210 50.000 0.00 0.0 33.07 4.35 R
2220 4057 2.054453 GGTGGAAGGCTTGGGCATC 61.054 63.158 3.46 0.0 40.87 3.91 R
3687 5608 2.535788 CGGAGGGAGAGCGTCGTAG 61.536 68.421 0.00 0.0 0.00 3.51 R
4121 9478 4.248859 GAGATGGAGCGTATATGTGCATT 58.751 43.478 0.00 0.0 0.00 3.56 R
5107 10964 0.036010 CTTGGAGGCATCGTTCAGGT 60.036 55.000 0.00 0.0 0.00 4.00 R
5880 11808 0.252513 TCTAACCCTAGCCAGCCACA 60.253 55.000 0.00 0.0 0.00 4.17 R
7154 13360 2.363680 TCGGCTTTCCAAAATTCTGCAA 59.636 40.909 0.00 0.0 0.00 4.08 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
80 178 1.888512 GGGAGAATGAGTGCAAAGCAA 59.111 47.619 0.00 0.00 41.47 3.91
96 194 6.435277 TGCAAAGCAAGAAGGAAGAAGAATAT 59.565 34.615 0.00 0.00 34.76 1.28
98 196 8.462016 GCAAAGCAAGAAGGAAGAAGAATATAA 58.538 33.333 0.00 0.00 0.00 0.98
123 221 9.987726 AATATGGAGAAAAGGAGAAAGAAGATT 57.012 29.630 0.00 0.00 0.00 2.40
124 222 9.987726 ATATGGAGAAAAGGAGAAAGAAGATTT 57.012 29.630 0.00 0.00 0.00 2.17
126 224 9.987726 ATGGAGAAAAGGAGAAAGAAGATTTAT 57.012 29.630 0.00 0.00 0.00 1.40
127 225 9.813826 TGGAGAAAAGGAGAAAGAAGATTTATT 57.186 29.630 0.00 0.00 0.00 1.40
157 255 9.434275 TTTTAGGGAAAAAGGAGAAAGAAGATT 57.566 29.630 0.00 0.00 32.05 2.40
158 256 9.434275 TTTAGGGAAAAAGGAGAAAGAAGATTT 57.566 29.630 0.00 0.00 0.00 2.17
159 257 7.921041 AGGGAAAAAGGAGAAAGAAGATTTT 57.079 32.000 0.00 0.00 0.00 1.82
160 258 8.324191 AGGGAAAAAGGAGAAAGAAGATTTTT 57.676 30.769 0.00 0.00 33.78 1.94
258 356 2.047560 GGGCCACTTACTCGCGTT 60.048 61.111 4.39 0.00 0.00 4.84
259 357 1.216178 GGGCCACTTACTCGCGTTA 59.784 57.895 4.39 0.00 0.00 3.18
260 358 1.080435 GGGCCACTTACTCGCGTTAC 61.080 60.000 4.39 0.00 0.00 2.50
261 359 1.408474 GGCCACTTACTCGCGTTACG 61.408 60.000 5.77 0.00 45.62 3.18
272 370 3.223854 CGTTACGACGCGTTTGGT 58.776 55.556 15.53 14.81 43.03 3.67
273 371 1.126438 CGTTACGACGCGTTTGGTC 59.874 57.895 15.53 0.00 43.03 4.02
278 376 2.659244 GACGCGTTTGGTCGTCCA 60.659 61.111 15.53 0.00 46.50 4.02
279 377 2.654912 GACGCGTTTGGTCGTCCAG 61.655 63.158 15.53 0.00 46.50 3.86
280 378 4.072088 CGCGTTTGGTCGTCCAGC 62.072 66.667 0.00 1.50 45.22 4.85
281 379 2.970324 GCGTTTGGTCGTCCAGCA 60.970 61.111 0.74 0.00 45.22 4.41
282 380 2.539338 GCGTTTGGTCGTCCAGCAA 61.539 57.895 0.74 0.00 45.22 3.91
283 381 1.569493 CGTTTGGTCGTCCAGCAAG 59.431 57.895 0.74 0.00 43.36 4.01
284 382 0.878523 CGTTTGGTCGTCCAGCAAGA 60.879 55.000 0.74 0.00 43.36 3.02
285 383 0.868406 GTTTGGTCGTCCAGCAAGAG 59.132 55.000 0.74 0.00 43.36 2.85
286 384 0.250295 TTTGGTCGTCCAGCAAGAGG 60.250 55.000 0.74 0.00 43.36 3.69
321 419 3.643792 CCATTCCACCAAAAACCCTACAA 59.356 43.478 0.00 0.00 0.00 2.41
322 420 4.502431 CCATTCCACCAAAAACCCTACAAC 60.502 45.833 0.00 0.00 0.00 3.32
323 421 2.668625 TCCACCAAAAACCCTACAACC 58.331 47.619 0.00 0.00 0.00 3.77
324 422 1.689813 CCACCAAAAACCCTACAACCC 59.310 52.381 0.00 0.00 0.00 4.11
325 423 1.689813 CACCAAAAACCCTACAACCCC 59.310 52.381 0.00 0.00 0.00 4.95
326 424 1.576757 ACCAAAAACCCTACAACCCCT 59.423 47.619 0.00 0.00 0.00 4.79
327 425 2.790585 ACCAAAAACCCTACAACCCCTA 59.209 45.455 0.00 0.00 0.00 3.53
328 426 3.207093 ACCAAAAACCCTACAACCCCTAA 59.793 43.478 0.00 0.00 0.00 2.69
329 427 4.224762 CCAAAAACCCTACAACCCCTAAA 58.775 43.478 0.00 0.00 0.00 1.85
330 428 4.654724 CCAAAAACCCTACAACCCCTAAAA 59.345 41.667 0.00 0.00 0.00 1.52
331 429 5.130643 CCAAAAACCCTACAACCCCTAAAAA 59.869 40.000 0.00 0.00 0.00 1.94
382 481 0.670854 GTCCACTCGCTCCCTGTTTC 60.671 60.000 0.00 0.00 0.00 2.78
1143 2909 1.749638 CGAGGCTACCGAGTGGAGT 60.750 63.158 0.00 0.00 39.21 3.85
1203 3008 2.665603 GAGGAGACAGGGCACACC 59.334 66.667 0.00 0.00 40.67 4.16
1258 3072 3.157932 AGTCGAGCAGAAGAATAGTGC 57.842 47.619 0.00 0.00 37.48 4.40
1383 3203 6.605119 CATGGGGGATTCTAAACTCTATGTT 58.395 40.000 0.00 0.00 41.29 2.71
1384 3204 7.691791 GCATGGGGGATTCTAAACTCTATGTTA 60.692 40.741 0.00 0.00 38.03 2.41
1600 3420 4.196193 CCTGTTCACAGTTGAGGTTTGTA 58.804 43.478 6.22 0.00 42.27 2.41
1694 3514 4.521639 TCGAGGTACTAGCTTCTTTGAACA 59.478 41.667 0.00 0.00 41.55 3.18
1697 3517 4.938226 AGGTACTAGCTTCTTTGAACATGC 59.062 41.667 0.00 0.00 36.02 4.06
1903 3740 1.871080 ATATTGCTGCAGCGGTAGAC 58.129 50.000 32.11 6.25 45.83 2.59
2085 3922 7.572523 TTCATAATGGGTCTAATGAAGCAAG 57.427 36.000 0.00 0.00 34.34 4.01
2097 3934 8.129211 GTCTAATGAAGCAAGTTTAGTGTTGTT 58.871 33.333 0.00 0.00 0.00 2.83
2220 4057 3.405831 TGACTCTGGAAACTCAGCAATG 58.594 45.455 0.00 0.00 34.91 2.82
2771 4663 5.294552 GGAGCAGTAGCCTAAAATACACAAG 59.705 44.000 0.00 0.00 43.56 3.16
2842 4735 7.447374 ACATAAGCTATGTGCAAGTAACAAA 57.553 32.000 7.69 0.00 46.94 2.83
3375 5285 3.696051 TGAAGCCCAAAAGAGATGTATGC 59.304 43.478 0.00 0.00 0.00 3.14
3758 5684 1.352622 TTGTGTGCTCCTCCCCTTGT 61.353 55.000 0.00 0.00 0.00 3.16
3790 5716 1.277557 GCTGTTGTGATCCTCCTCTGT 59.722 52.381 0.00 0.00 0.00 3.41
3973 9326 1.606889 AACCTCGGCTCGACTCCTT 60.607 57.895 0.00 0.00 0.00 3.36
3986 9340 5.679894 GCTCGACTCCTTGACTCATAATTCA 60.680 44.000 0.00 0.00 0.00 2.57
4487 10030 8.971073 CAATTATATCTTCCCAAGTGAAAACCT 58.029 33.333 0.00 0.00 0.00 3.50
4595 10442 8.514594 CAACATTTTGTGTATTCAGAGTATGGT 58.485 33.333 0.00 0.00 41.14 3.55
4757 10612 7.748691 ACATAAGCATGTGTATCATTGCATA 57.251 32.000 0.00 0.00 43.89 3.14
4759 10614 8.631797 ACATAAGCATGTGTATCATTGCATAAA 58.368 29.630 0.00 0.00 43.89 1.40
4795 10650 2.263021 GCCGGGTACAACGCCTTTT 61.263 57.895 2.18 0.00 0.00 2.27
4840 10696 0.704076 ATAGCAACCACACCCACCAT 59.296 50.000 0.00 0.00 0.00 3.55
4849 10705 1.214305 ACACCCACCATGCCTACCAT 61.214 55.000 0.00 0.00 33.39 3.55
4870 10726 2.236893 TGATGCATGCTTCACCTAGTCA 59.763 45.455 27.21 7.55 0.00 3.41
4979 10836 1.686052 TCCATGACAAGCCAAACCAAC 59.314 47.619 0.00 0.00 0.00 3.77
5026 10883 0.532862 AGTTGACAAGTGGACGGCAG 60.533 55.000 0.00 0.00 0.00 4.85
5067 10924 1.298788 GCGTCTTCTAGAGAGCGGC 60.299 63.158 11.79 0.00 34.31 6.53
5107 10964 0.979665 CTCAGGGACTCCTTGAGCAA 59.020 55.000 21.00 0.00 42.67 3.91
5114 10971 2.147150 GACTCCTTGAGCAACCTGAAC 58.853 52.381 0.00 0.00 32.04 3.18
5116 10973 0.756294 TCCTTGAGCAACCTGAACGA 59.244 50.000 0.00 0.00 0.00 3.85
5117 10974 1.347707 TCCTTGAGCAACCTGAACGAT 59.652 47.619 0.00 0.00 0.00 3.73
5149 11006 0.529992 GGGACGACTCCATAAAGCCG 60.530 60.000 0.00 0.00 38.52 5.52
5152 11009 2.159198 GGACGACTCCATAAAGCCGTTA 60.159 50.000 0.00 0.00 36.42 3.18
5153 11010 3.514645 GACGACTCCATAAAGCCGTTAA 58.485 45.455 0.00 0.00 0.00 2.01
5154 11011 4.117685 GACGACTCCATAAAGCCGTTAAT 58.882 43.478 0.00 0.00 0.00 1.40
5157 11014 2.949644 ACTCCATAAAGCCGTTAATGCC 59.050 45.455 0.00 0.00 0.00 4.40
5165 11022 1.817941 CCGTTAATGCCTGGTCCGG 60.818 63.158 0.00 0.00 0.00 5.14
5180 11037 1.215647 CCGGAGAGTCGAACCAAGG 59.784 63.158 0.00 0.00 0.00 3.61
5214 11071 1.918293 AAGGGGCGTCATGGTCAGA 60.918 57.895 0.00 0.00 0.00 3.27
5221 11078 1.081892 CGTCATGGTCAGAGCCAAAG 58.918 55.000 0.00 0.00 42.48 2.77
5222 11079 1.338105 CGTCATGGTCAGAGCCAAAGA 60.338 52.381 0.00 0.00 42.48 2.52
5223 11080 2.079925 GTCATGGTCAGAGCCAAAGAC 58.920 52.381 0.00 5.10 42.48 3.01
5301 11198 1.053424 AAAGCCCAACGTCCACTAGA 58.947 50.000 0.00 0.00 0.00 2.43
5327 11224 0.468029 CAAGAAGGCCAACCACCACT 60.468 55.000 5.01 0.00 39.06 4.00
5332 11229 2.359478 GCCAACCACCACTACGGG 60.359 66.667 0.00 0.00 40.22 5.28
5346 11243 1.381928 TACGGGAGGAGTCGCATCAC 61.382 60.000 0.00 0.00 35.33 3.06
5365 11262 0.810648 CGTAGCATTGCAACCACCAT 59.189 50.000 11.91 0.00 0.00 3.55
5374 11271 1.966762 CAACCACCATCACCAAGCC 59.033 57.895 0.00 0.00 0.00 4.35
5392 11289 1.134401 GCCGACCAAATCTGGATCAGA 60.134 52.381 0.00 0.00 46.92 3.27
5400 11297 5.198965 CCAAATCTGGATCAGAGAAACCAT 58.801 41.667 3.94 0.00 46.92 3.55
5401 11298 5.067413 CCAAATCTGGATCAGAGAAACCATG 59.933 44.000 3.94 0.00 46.92 3.66
5436 11333 2.202298 GCAACCAAATCGACGCCG 60.202 61.111 0.00 0.00 37.07 6.46
5438 11335 3.428282 AACCAAATCGACGCCGGC 61.428 61.111 19.07 19.07 36.24 6.13
5461 11358 4.100084 CTCCCAGCACCATGCCGA 62.100 66.667 0.00 0.00 46.52 5.54
5480 11377 2.498167 GACAAGAGCACCACAACATCT 58.502 47.619 0.00 0.00 0.00 2.90
5481 11378 2.224606 ACAAGAGCACCACAACATCTG 58.775 47.619 0.00 0.00 0.00 2.90
5507 11404 1.677052 GTTACTACGAGGAGAGCCCAG 59.323 57.143 0.00 0.00 37.41 4.45
5508 11405 1.210538 TACTACGAGGAGAGCCCAGA 58.789 55.000 0.00 0.00 37.41 3.86
5520 11417 3.781307 CCCAGACCCGCCATCGAA 61.781 66.667 0.00 0.00 38.10 3.71
5524 11421 2.884207 GACCCGCCATCGAACGTC 60.884 66.667 0.00 0.00 38.10 4.34
5540 11437 2.203084 TCGAACCGCTGGCACAAA 60.203 55.556 0.00 0.00 38.70 2.83
5645 11544 0.942962 GGATCTCCGAAGCTGCAATG 59.057 55.000 1.02 0.00 0.00 2.82
5647 11546 0.465097 ATCTCCGAAGCTGCAATGGG 60.465 55.000 1.02 1.03 0.00 4.00
5655 11554 1.283347 AGCTGCAATGGGAGAGAGAA 58.717 50.000 1.02 0.00 33.71 2.87
5670 11569 2.980233 GAACGCCAAGCTGCAGGT 60.980 61.111 13.85 13.85 0.00 4.00
5769 11691 1.515521 GCACAGGTTCCCAAACTCCG 61.516 60.000 0.00 0.00 35.61 4.63
5784 11706 3.361977 CCGCCCAAAACTCCACCG 61.362 66.667 0.00 0.00 0.00 4.94
5785 11707 3.361977 CGCCCAAAACTCCACCGG 61.362 66.667 0.00 0.00 0.00 5.28
5792 11714 1.720694 AAAACTCCACCGGTTGCACG 61.721 55.000 2.97 0.00 0.00 5.34
5980 11908 4.277423 ACCGGGTTGTTTAAGTTTGAGATG 59.723 41.667 6.32 0.00 0.00 2.90
5999 11927 6.016024 TGAGATGAATTCAAGTCAAACCAAGG 60.016 38.462 13.09 0.00 0.00 3.61
6000 11928 4.935352 TGAATTCAAGTCAAACCAAGGG 57.065 40.909 5.45 0.00 0.00 3.95
6001 11929 4.285863 TGAATTCAAGTCAAACCAAGGGT 58.714 39.130 5.45 0.00 37.65 4.34
6002 11930 5.450453 TGAATTCAAGTCAAACCAAGGGTA 58.550 37.500 5.45 0.00 33.12 3.69
6054 11985 3.865745 CCTTGCATAACCTTCTACACTCG 59.134 47.826 0.00 0.00 0.00 4.18
6063 11994 3.215151 CCTTCTACACTCGAGGCATCTA 58.785 50.000 18.41 0.00 0.00 1.98
6064 11995 3.632604 CCTTCTACACTCGAGGCATCTAA 59.367 47.826 18.41 3.03 0.00 2.10
6065 11996 4.098044 CCTTCTACACTCGAGGCATCTAAA 59.902 45.833 18.41 1.46 0.00 1.85
6066 11997 5.221342 CCTTCTACACTCGAGGCATCTAAAT 60.221 44.000 18.41 0.00 0.00 1.40
6067 11998 5.854010 TCTACACTCGAGGCATCTAAATT 57.146 39.130 18.41 0.00 0.00 1.82
6068 11999 5.833082 TCTACACTCGAGGCATCTAAATTC 58.167 41.667 18.41 0.00 0.00 2.17
6069 12000 3.448686 ACACTCGAGGCATCTAAATTCG 58.551 45.455 18.41 0.00 0.00 3.34
6070 12001 3.130516 ACACTCGAGGCATCTAAATTCGA 59.869 43.478 18.41 0.00 37.89 3.71
6072 12003 3.371102 TCGAGGCATCTAAATTCGAGG 57.629 47.619 0.00 0.00 35.60 4.63
6073 12004 1.795286 CGAGGCATCTAAATTCGAGGC 59.205 52.381 0.00 5.96 37.45 4.70
6074 12005 2.803133 CGAGGCATCTAAATTCGAGGCA 60.803 50.000 13.83 0.00 39.72 4.75
6075 12006 2.805099 GAGGCATCTAAATTCGAGGCAG 59.195 50.000 13.83 0.00 39.72 4.85
6076 12007 1.265365 GGCATCTAAATTCGAGGCAGC 59.735 52.381 13.83 0.00 39.72 5.25
6077 12008 2.216898 GCATCTAAATTCGAGGCAGCT 58.783 47.619 8.81 0.00 38.03 4.24
6078 12009 3.393800 GCATCTAAATTCGAGGCAGCTA 58.606 45.455 8.81 0.00 38.03 3.32
6079 12010 3.809832 GCATCTAAATTCGAGGCAGCTAA 59.190 43.478 8.81 0.00 38.03 3.09
6080 12011 4.273480 GCATCTAAATTCGAGGCAGCTAAA 59.727 41.667 8.81 0.00 38.03 1.85
6081 12012 5.742446 CATCTAAATTCGAGGCAGCTAAAC 58.258 41.667 0.00 0.00 0.00 2.01
6082 12013 4.827692 TCTAAATTCGAGGCAGCTAAACA 58.172 39.130 0.00 0.00 0.00 2.83
6083 12014 5.428253 TCTAAATTCGAGGCAGCTAAACAT 58.572 37.500 0.00 0.00 0.00 2.71
6084 12015 5.880332 TCTAAATTCGAGGCAGCTAAACATT 59.120 36.000 0.00 0.00 0.00 2.71
6085 12016 4.622701 AATTCGAGGCAGCTAAACATTC 57.377 40.909 0.00 0.00 0.00 2.67
6086 12017 3.334583 TTCGAGGCAGCTAAACATTCT 57.665 42.857 0.00 0.00 0.00 2.40
6087 12018 4.465632 TTCGAGGCAGCTAAACATTCTA 57.534 40.909 0.00 0.00 0.00 2.10
6088 12019 3.782046 TCGAGGCAGCTAAACATTCTAC 58.218 45.455 0.00 0.00 0.00 2.59
6089 12020 3.194755 TCGAGGCAGCTAAACATTCTACA 59.805 43.478 0.00 0.00 0.00 2.74
6090 12021 3.307242 CGAGGCAGCTAAACATTCTACAC 59.693 47.826 0.00 0.00 0.00 2.90
6091 12022 4.508662 GAGGCAGCTAAACATTCTACACT 58.491 43.478 0.00 0.00 0.00 3.55
6092 12023 4.508662 AGGCAGCTAAACATTCTACACTC 58.491 43.478 0.00 0.00 0.00 3.51
6093 12024 4.020218 AGGCAGCTAAACATTCTACACTCA 60.020 41.667 0.00 0.00 0.00 3.41
6094 12025 4.695455 GGCAGCTAAACATTCTACACTCAA 59.305 41.667 0.00 0.00 0.00 3.02
6095 12026 5.163814 GGCAGCTAAACATTCTACACTCAAG 60.164 44.000 0.00 0.00 0.00 3.02
6096 12027 5.163814 GCAGCTAAACATTCTACACTCAAGG 60.164 44.000 0.00 0.00 0.00 3.61
6097 12028 4.938226 AGCTAAACATTCTACACTCAAGGC 59.062 41.667 0.00 0.00 0.00 4.35
6098 12029 4.695455 GCTAAACATTCTACACTCAAGGCA 59.305 41.667 0.00 0.00 0.00 4.75
6099 12030 5.355350 GCTAAACATTCTACACTCAAGGCAT 59.645 40.000 0.00 0.00 0.00 4.40
6100 12031 5.886960 AAACATTCTACACTCAAGGCATC 57.113 39.130 0.00 0.00 0.00 3.91
6101 12032 4.833478 ACATTCTACACTCAAGGCATCT 57.167 40.909 0.00 0.00 0.00 2.90
6165 12096 8.944212 AGCAAATTTTGTACATACGTTCTTAC 57.056 30.769 10.65 0.00 0.00 2.34
6307 12242 1.300963 GCCACTGCAATGAGAGGGA 59.699 57.895 0.00 0.00 37.47 4.20
6316 12255 2.373169 GCAATGAGAGGGACCATCCATA 59.627 50.000 1.65 0.00 38.64 2.74
6338 12277 1.302033 CACGAAGAACCTGCTGCCT 60.302 57.895 0.00 0.00 0.00 4.75
6407 12346 9.396022 CTTATTAACCTGTACAACAATGATCCT 57.604 33.333 0.00 0.00 0.00 3.24
6452 12391 6.372381 TCATGTTTGATGTCACTGTATCCTTG 59.628 38.462 0.00 0.00 0.00 3.61
6462 12401 4.283467 TCACTGTATCCTTGTTACTGCAGT 59.717 41.667 25.12 25.12 36.53 4.40
6644 12594 4.689612 TGGATACAGAGAAATGGTAGCC 57.310 45.455 0.00 0.00 46.17 3.93
6652 12602 5.189736 ACAGAGAAATGGTAGCCTTGTATCA 59.810 40.000 0.00 0.00 0.00 2.15
6696 12646 8.818057 AGCGTCACTATAATTACAAGATTGTTC 58.182 33.333 3.14 0.00 42.35 3.18
6697 12647 8.818057 GCGTCACTATAATTACAAGATTGTTCT 58.182 33.333 3.14 0.00 42.35 3.01
6929 13052 4.627741 GCATGTAAATCCCTGTCCACCTAA 60.628 45.833 0.00 0.00 0.00 2.69
6938 13061 3.885297 CCCTGTCCACCTAAATTGCATAG 59.115 47.826 0.00 0.00 0.00 2.23
6958 13081 8.686334 TGCATAGAGAACCTTTTTCCATATTTC 58.314 33.333 0.00 0.00 0.00 2.17
6991 13114 1.927371 GGAAAGGAGGATTAACCCCCA 59.073 52.381 0.00 0.00 40.05 4.96
7002 13125 0.116143 TAACCCCCAGGCTTTGCATT 59.884 50.000 0.00 0.00 36.11 3.56
7107 13313 4.637600 ACCCAGTGGTATCCAAAGGTATA 58.362 43.478 8.74 0.00 45.45 1.47
7108 13314 5.232347 ACCCAGTGGTATCCAAAGGTATAT 58.768 41.667 8.74 0.00 45.45 0.86
7135 13341 9.236006 GAATGAATATGTAGGCTTGGACATAAT 57.764 33.333 11.50 4.80 40.83 1.28
7138 13344 8.217111 TGAATATGTAGGCTTGGACATAATTCA 58.783 33.333 11.50 15.47 40.83 2.57
7165 13371 7.141363 GTGTTAGATCACAGTTGCAGAATTTT 58.859 34.615 0.00 0.00 38.12 1.82
7174 13380 2.437200 TGCAGAATTTTGGAAAGCCG 57.563 45.000 0.00 0.00 36.79 5.52
7175 13381 1.959985 TGCAGAATTTTGGAAAGCCGA 59.040 42.857 0.00 0.00 36.79 5.54
7176 13382 2.030007 TGCAGAATTTTGGAAAGCCGAG 60.030 45.455 0.00 0.00 36.79 4.63
7177 13383 2.029918 GCAGAATTTTGGAAAGCCGAGT 60.030 45.455 0.00 0.00 36.79 4.18
7178 13384 3.826466 CAGAATTTTGGAAAGCCGAGTC 58.174 45.455 0.00 0.00 36.79 3.36
7179 13385 3.503748 CAGAATTTTGGAAAGCCGAGTCT 59.496 43.478 0.00 0.00 36.79 3.24
7180 13386 3.503748 AGAATTTTGGAAAGCCGAGTCTG 59.496 43.478 0.00 0.00 36.79 3.51
7181 13387 2.341846 TTTTGGAAAGCCGAGTCTGT 57.658 45.000 0.00 0.00 36.79 3.41
7182 13388 2.341846 TTTGGAAAGCCGAGTCTGTT 57.658 45.000 0.00 0.00 36.79 3.16
7183 13389 3.478857 TTTGGAAAGCCGAGTCTGTTA 57.521 42.857 0.00 0.00 36.79 2.41
7184 13390 3.478857 TTGGAAAGCCGAGTCTGTTAA 57.521 42.857 0.00 0.00 36.79 2.01
7185 13391 3.695830 TGGAAAGCCGAGTCTGTTAAT 57.304 42.857 0.00 0.00 36.79 1.40
7186 13392 4.015872 TGGAAAGCCGAGTCTGTTAATT 57.984 40.909 0.00 0.00 36.79 1.40
7187 13393 4.394729 TGGAAAGCCGAGTCTGTTAATTT 58.605 39.130 0.00 0.00 36.79 1.82
7188 13394 4.825085 TGGAAAGCCGAGTCTGTTAATTTT 59.175 37.500 0.00 0.00 36.79 1.82
7189 13395 5.154222 GGAAAGCCGAGTCTGTTAATTTTG 58.846 41.667 0.00 0.00 0.00 2.44
7190 13396 3.831715 AGCCGAGTCTGTTAATTTTGC 57.168 42.857 0.00 0.00 0.00 3.68
7191 13397 3.146066 AGCCGAGTCTGTTAATTTTGCA 58.854 40.909 0.00 0.00 0.00 4.08
7192 13398 3.758554 AGCCGAGTCTGTTAATTTTGCAT 59.241 39.130 0.00 0.00 0.00 3.96
7193 13399 4.098416 GCCGAGTCTGTTAATTTTGCATC 58.902 43.478 0.00 0.00 0.00 3.91
7194 13400 4.142600 GCCGAGTCTGTTAATTTTGCATCT 60.143 41.667 0.00 0.00 0.00 2.90
7195 13401 5.064707 GCCGAGTCTGTTAATTTTGCATCTA 59.935 40.000 0.00 0.00 0.00 1.98
7196 13402 6.478588 CCGAGTCTGTTAATTTTGCATCTAC 58.521 40.000 0.00 0.00 0.00 2.59
7197 13403 6.092122 CCGAGTCTGTTAATTTTGCATCTACA 59.908 38.462 0.00 0.00 0.00 2.74
7198 13404 7.360861 CCGAGTCTGTTAATTTTGCATCTACAA 60.361 37.037 0.00 0.00 0.00 2.41
7199 13405 8.177663 CGAGTCTGTTAATTTTGCATCTACAAT 58.822 33.333 0.00 0.00 0.00 2.71
7200 13406 9.495754 GAGTCTGTTAATTTTGCATCTACAATC 57.504 33.333 0.00 0.00 0.00 2.67
7201 13407 9.236006 AGTCTGTTAATTTTGCATCTACAATCT 57.764 29.630 0.00 0.00 0.00 2.40
7230 13436 8.200792 ACTACAAATACCTGTCTCATTCAGATC 58.799 37.037 0.00 0.00 35.20 2.75
7242 13448 8.526978 TGTCTCATTCAGATCTAATACATAGGC 58.473 37.037 0.00 0.00 32.08 3.93
7300 13506 6.317140 ACAGTATACTCATTCCACTTGCATTG 59.683 38.462 1.26 0.00 0.00 2.82
7301 13507 6.317140 CAGTATACTCATTCCACTTGCATTGT 59.683 38.462 1.26 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.388065 CGGTCCTTCTCTGGCTCGAT 61.388 60.000 0.00 0.00 0.00 3.59
1 2 2.046864 CGGTCCTTCTCTGGCTCGA 61.047 63.158 0.00 0.00 0.00 4.04
50 51 3.411517 ATTCTCCCCGCCCACCAG 61.412 66.667 0.00 0.00 0.00 4.00
98 196 9.987726 AAATCTTCTTTCTCCTTTTCTCCATAT 57.012 29.630 0.00 0.00 0.00 1.78
100 198 9.987726 ATAAATCTTCTTTCTCCTTTTCTCCAT 57.012 29.630 0.00 0.00 0.00 3.41
101 199 9.813826 AATAAATCTTCTTTCTCCTTTTCTCCA 57.186 29.630 0.00 0.00 0.00 3.86
129 227 9.434275 TCTTCTTTCTCCTTTTTCCCTAAAAAT 57.566 29.630 0.00 0.00 42.22 1.82
180 278 9.029368 CCTTTCTCCATCTTATTTCTCCTTTTT 57.971 33.333 0.00 0.00 0.00 1.94
181 279 7.617329 CCCTTTCTCCATCTTATTTCTCCTTTT 59.383 37.037 0.00 0.00 0.00 2.27
182 280 7.036571 TCCCTTTCTCCATCTTATTTCTCCTTT 60.037 37.037 0.00 0.00 0.00 3.11
183 281 6.448387 TCCCTTTCTCCATCTTATTTCTCCTT 59.552 38.462 0.00 0.00 0.00 3.36
184 282 5.973124 TCCCTTTCTCCATCTTATTTCTCCT 59.027 40.000 0.00 0.00 0.00 3.69
185 283 6.100424 TCTCCCTTTCTCCATCTTATTTCTCC 59.900 42.308 0.00 0.00 0.00 3.71
186 284 7.130681 TCTCCCTTTCTCCATCTTATTTCTC 57.869 40.000 0.00 0.00 0.00 2.87
187 285 7.516450 TTCTCCCTTTCTCCATCTTATTTCT 57.484 36.000 0.00 0.00 0.00 2.52
188 286 8.759481 ATTTCTCCCTTTCTCCATCTTATTTC 57.241 34.615 0.00 0.00 0.00 2.17
193 291 9.859152 CTTATTATTTCTCCCTTTCTCCATCTT 57.141 33.333 0.00 0.00 0.00 2.40
194 292 7.941790 GCTTATTATTTCTCCCTTTCTCCATCT 59.058 37.037 0.00 0.00 0.00 2.90
195 293 7.175816 GGCTTATTATTTCTCCCTTTCTCCATC 59.824 40.741 0.00 0.00 0.00 3.51
196 294 7.007116 GGCTTATTATTTCTCCCTTTCTCCAT 58.993 38.462 0.00 0.00 0.00 3.41
197 295 6.365520 GGCTTATTATTTCTCCCTTTCTCCA 58.634 40.000 0.00 0.00 0.00 3.86
198 296 5.470437 CGGCTTATTATTTCTCCCTTTCTCC 59.530 44.000 0.00 0.00 0.00 3.71
199 297 5.049336 GCGGCTTATTATTTCTCCCTTTCTC 60.049 44.000 0.00 0.00 0.00 2.87
200 298 4.822350 GCGGCTTATTATTTCTCCCTTTCT 59.178 41.667 0.00 0.00 0.00 2.52
201 299 4.822350 AGCGGCTTATTATTTCTCCCTTTC 59.178 41.667 0.00 0.00 0.00 2.62
202 300 4.580580 CAGCGGCTTATTATTTCTCCCTTT 59.419 41.667 0.00 0.00 0.00 3.11
203 301 4.137543 CAGCGGCTTATTATTTCTCCCTT 58.862 43.478 0.00 0.00 0.00 3.95
204 302 3.496870 CCAGCGGCTTATTATTTCTCCCT 60.497 47.826 0.00 0.00 0.00 4.20
205 303 2.814336 CCAGCGGCTTATTATTTCTCCC 59.186 50.000 0.00 0.00 0.00 4.30
216 314 2.605535 ATCTCCCCTCCAGCGGCTTA 62.606 60.000 0.00 0.00 0.00 3.09
262 360 2.660552 CTGGACGACCAAACGCGT 60.661 61.111 5.58 5.58 46.32 6.01
263 361 4.072088 GCTGGACGACCAAACGCG 62.072 66.667 3.53 3.53 46.32 6.01
264 362 2.443957 CTTGCTGGACGACCAAACGC 62.444 60.000 8.23 8.77 46.32 4.84
265 363 0.878523 TCTTGCTGGACGACCAAACG 60.879 55.000 8.23 0.00 46.32 3.60
266 364 0.868406 CTCTTGCTGGACGACCAAAC 59.132 55.000 8.23 3.93 46.32 2.93
267 365 0.250295 CCTCTTGCTGGACGACCAAA 60.250 55.000 8.23 0.00 46.32 3.28
268 366 1.371183 CCTCTTGCTGGACGACCAA 59.629 57.895 8.23 0.00 46.32 3.67
269 367 3.059982 CCTCTTGCTGGACGACCA 58.940 61.111 6.42 6.42 44.76 4.02
270 368 2.435059 GCCTCTTGCTGGACGACC 60.435 66.667 0.00 0.00 36.87 4.79
271 369 1.739562 CTGCCTCTTGCTGGACGAC 60.740 63.158 0.00 0.00 42.00 4.34
272 370 0.898326 TACTGCCTCTTGCTGGACGA 60.898 55.000 0.00 0.00 42.74 4.20
273 371 0.459237 CTACTGCCTCTTGCTGGACG 60.459 60.000 0.00 0.00 42.74 4.79
274 372 0.742635 GCTACTGCCTCTTGCTGGAC 60.743 60.000 0.00 0.00 42.74 4.02
275 373 1.599047 GCTACTGCCTCTTGCTGGA 59.401 57.895 0.00 0.00 42.74 3.86
276 374 1.812922 CGCTACTGCCTCTTGCTGG 60.813 63.158 0.00 0.00 42.74 4.85
277 375 2.459442 GCGCTACTGCCTCTTGCTG 61.459 63.158 0.00 0.00 43.93 4.41
278 376 2.125350 GCGCTACTGCCTCTTGCT 60.125 61.111 0.00 0.00 42.00 3.91
279 377 2.434884 TGCGCTACTGCCTCTTGC 60.435 61.111 9.73 0.00 41.77 4.01
280 378 2.459442 GCTGCGCTACTGCCTCTTG 61.459 63.158 9.73 0.00 37.26 3.02
281 379 2.125350 GCTGCGCTACTGCCTCTT 60.125 61.111 9.73 0.00 37.26 2.85
286 384 2.825836 AATGGGCTGCGCTACTGC 60.826 61.111 17.81 7.84 42.19 4.40
331 429 7.214381 GCTTATCTGTAGGGTTTTTGGTTTTT 58.786 34.615 0.00 0.00 0.00 1.94
332 430 6.516028 CGCTTATCTGTAGGGTTTTTGGTTTT 60.516 38.462 0.00 0.00 0.00 2.43
333 431 5.048294 CGCTTATCTGTAGGGTTTTTGGTTT 60.048 40.000 0.00 0.00 0.00 3.27
334 432 4.457949 CGCTTATCTGTAGGGTTTTTGGTT 59.542 41.667 0.00 0.00 0.00 3.67
335 433 4.007659 CGCTTATCTGTAGGGTTTTTGGT 58.992 43.478 0.00 0.00 0.00 3.67
336 434 4.007659 ACGCTTATCTGTAGGGTTTTTGG 58.992 43.478 0.00 0.00 35.53 3.28
337 435 4.454504 ACACGCTTATCTGTAGGGTTTTTG 59.545 41.667 0.00 0.00 36.75 2.44
338 436 4.454504 CACACGCTTATCTGTAGGGTTTTT 59.545 41.667 0.00 0.00 36.75 1.94
339 437 4.000988 CACACGCTTATCTGTAGGGTTTT 58.999 43.478 0.00 0.00 36.75 2.43
340 438 3.259876 TCACACGCTTATCTGTAGGGTTT 59.740 43.478 0.00 0.00 36.75 3.27
341 439 2.829720 TCACACGCTTATCTGTAGGGTT 59.170 45.455 0.00 0.00 36.75 4.11
342 440 2.427453 CTCACACGCTTATCTGTAGGGT 59.573 50.000 0.00 0.00 39.10 4.34
343 441 2.427453 ACTCACACGCTTATCTGTAGGG 59.573 50.000 0.00 0.00 0.00 3.53
344 442 3.489398 GGACTCACACGCTTATCTGTAGG 60.489 52.174 0.00 0.00 0.00 3.18
345 443 3.128764 TGGACTCACACGCTTATCTGTAG 59.871 47.826 0.00 0.00 0.00 2.74
346 444 3.086282 TGGACTCACACGCTTATCTGTA 58.914 45.455 0.00 0.00 0.00 2.74
347 445 1.893137 TGGACTCACACGCTTATCTGT 59.107 47.619 0.00 0.00 0.00 3.41
348 446 2.094494 AGTGGACTCACACGCTTATCTG 60.094 50.000 0.00 0.00 45.91 2.90
852 2616 0.456312 GTGTGTAGAAGAGGACGCGG 60.456 60.000 12.47 0.00 0.00 6.46
853 2617 0.456312 GGTGTGTAGAAGAGGACGCG 60.456 60.000 3.53 3.53 0.00 6.01
1203 3008 0.593773 CTTTGTTTCCCACAACCGCG 60.594 55.000 0.00 0.00 45.54 6.46
1258 3072 1.878522 GCTCGCCCACGTCATACAG 60.879 63.158 0.00 0.00 41.18 2.74
1383 3203 3.311778 TGGGACCATCCTCCATTAACCTA 60.312 47.826 0.00 0.00 36.57 3.08
1384 3204 2.136026 GGGACCATCCTCCATTAACCT 58.864 52.381 0.00 0.00 36.57 3.50
1437 3257 0.790207 GCGATGTTTGAAGCTCGACA 59.210 50.000 0.00 0.00 33.07 4.35
1496 3316 2.946990 CCACCACTTACGAAGGTTTTGT 59.053 45.455 0.00 0.00 32.15 2.83
1509 3329 2.526873 AGCGAGGGTCCACCACTT 60.527 61.111 0.00 0.00 43.89 3.16
1600 3420 2.159179 ACCTTCTTTGTTTGGCCAGT 57.841 45.000 5.11 0.00 0.00 4.00
1811 3648 3.570125 TGCAAAACGGTGTCCAATTCATA 59.430 39.130 0.00 0.00 0.00 2.15
1903 3740 7.546667 AGGCAAAATGTTCTAATGTTAATGCTG 59.453 33.333 0.00 0.00 0.00 4.41
1963 3800 7.597288 AAAAGTTTAACCTAGCACAATCCTT 57.403 32.000 0.00 0.00 0.00 3.36
2071 3908 7.639945 ACAACACTAAACTTGCTTCATTAGAC 58.360 34.615 0.00 0.00 0.00 2.59
2168 4005 9.547279 AATACTCCCTCCATTTCAAAATAACTT 57.453 29.630 0.00 0.00 0.00 2.66
2193 4030 5.012046 TGCTGAGTTTCCAGAGTCAATCTAA 59.988 40.000 0.00 0.00 36.10 2.10
2220 4057 2.054453 GGTGGAAGGCTTGGGCATC 61.054 63.158 3.46 0.00 40.87 3.91
3687 5608 2.535788 CGGAGGGAGAGCGTCGTAG 61.536 68.421 0.00 0.00 0.00 3.51
3758 5684 4.350368 TCACAACAGCATAGGAGAACAA 57.650 40.909 0.00 0.00 0.00 2.83
4121 9478 4.248859 GAGATGGAGCGTATATGTGCATT 58.751 43.478 0.00 0.00 0.00 3.56
4218 9580 6.457355 TGCTTCATGTCATTTTGCTGTATTT 58.543 32.000 0.00 0.00 0.00 1.40
4279 9643 6.595716 GCTGTAGTTATCATGGTCTGTTCTTT 59.404 38.462 0.00 0.00 0.00 2.52
4405 9882 5.939883 TGAGTGTATGATTTTCACAAGGGAG 59.060 40.000 0.00 0.00 34.94 4.30
4487 10030 9.895138 GTAGTTTAATTAGTTCCCACCATCTTA 57.105 33.333 0.00 0.00 0.00 2.10
4595 10442 5.863965 TGAATCAGTTGGTCTCATGTACAA 58.136 37.500 0.00 0.00 0.00 2.41
4733 10588 6.644248 ATGCAATGATACACATGCTTATGT 57.356 33.333 0.00 0.00 39.39 2.29
4757 10612 2.630098 GCTTCTTTGCCCCTTCTTCTTT 59.370 45.455 0.00 0.00 0.00 2.52
4759 10614 1.548809 GGCTTCTTTGCCCCTTCTTCT 60.549 52.381 0.00 0.00 46.82 2.85
4795 10650 3.951680 TGAGATGAGCGTAGTAATGTCCA 59.048 43.478 0.00 0.00 0.00 4.02
4840 10696 2.723231 GCATGCATCATGGTAGGCA 58.277 52.632 14.21 0.00 41.64 4.75
4849 10705 2.236893 TGACTAGGTGAAGCATGCATCA 59.763 45.455 20.99 20.99 0.00 3.07
4930 10786 0.662619 TGTTGCAGAGGTTTTCAGCG 59.337 50.000 0.00 0.00 40.90 5.18
4988 10845 3.830192 CCTCTTGGCGCAATGGGC 61.830 66.667 14.21 14.21 40.84 5.36
5000 10857 3.741388 CGTCCACTTGTCAACTTCCTCTT 60.741 47.826 0.00 0.00 0.00 2.85
5054 10911 3.889044 CGCCGCCGCTCTCTAGAA 61.889 66.667 0.00 0.00 0.00 2.10
5057 10914 3.966104 CATCGCCGCCGCTCTCTA 61.966 66.667 0.00 0.00 0.00 2.43
5067 10924 1.351707 GCAATGTACACCATCGCCG 59.648 57.895 0.00 0.00 31.75 6.46
5076 10933 1.078497 CCCTGAGGCGCAATGTACA 60.078 57.895 10.83 0.00 0.00 2.90
5077 10934 1.090052 GTCCCTGAGGCGCAATGTAC 61.090 60.000 10.83 0.00 0.00 2.90
5107 10964 0.036010 CTTGGAGGCATCGTTCAGGT 60.036 55.000 0.00 0.00 0.00 4.00
5114 10971 2.507944 CCCTCCTTGGAGGCATCG 59.492 66.667 26.16 11.73 40.95 3.84
5116 10973 2.003548 GTCCCCTCCTTGGAGGCAT 61.004 63.158 26.16 0.00 40.95 4.40
5117 10974 2.610859 GTCCCCTCCTTGGAGGCA 60.611 66.667 26.16 14.15 40.95 4.75
5130 10987 0.529992 CGGCTTTATGGAGTCGTCCC 60.530 60.000 0.00 0.00 43.15 4.46
5149 11006 0.539986 TCTCCGGACCAGGCATTAAC 59.460 55.000 0.00 0.00 0.00 2.01
5152 11009 1.613630 ACTCTCCGGACCAGGCATT 60.614 57.895 0.00 0.00 0.00 3.56
5153 11010 2.039624 ACTCTCCGGACCAGGCAT 59.960 61.111 0.00 0.00 0.00 4.40
5154 11011 2.680352 GACTCTCCGGACCAGGCA 60.680 66.667 0.00 0.00 0.00 4.75
5157 11014 1.507174 GTTCGACTCTCCGGACCAG 59.493 63.158 0.00 1.33 32.11 4.00
5165 11022 2.414806 GAAACCCTTGGTTCGACTCTC 58.585 52.381 0.00 0.00 46.20 3.20
5301 11198 2.441750 TGGTTGGCCTTCTTGAGTAACT 59.558 45.455 3.32 0.00 35.27 2.24
5327 11224 1.077285 TGATGCGACTCCTCCCGTA 60.077 57.895 0.00 0.00 0.00 4.02
5332 11229 0.592754 GCTACGTGATGCGACTCCTC 60.593 60.000 0.00 0.00 44.77 3.71
5346 11243 0.810648 ATGGTGGTTGCAATGCTACG 59.189 50.000 13.05 0.00 35.33 3.51
5365 11262 0.400213 AGATTTGGTCGGCTTGGTGA 59.600 50.000 0.00 0.00 0.00 4.02
5374 11271 3.808466 TCTCTGATCCAGATTTGGTCG 57.192 47.619 1.59 0.00 45.26 4.79
5392 11289 2.436646 CGAGCCGGCATGGTTTCT 60.437 61.111 31.54 4.27 41.21 2.52
5449 11346 1.376424 CTCTTGTCGGCATGGTGCT 60.376 57.895 2.81 0.00 44.28 4.40
5461 11358 2.158769 TCAGATGTTGTGGTGCTCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
5507 11404 2.884207 GACGTTCGATGGCGGGTC 60.884 66.667 0.00 0.00 38.28 4.46
5508 11405 4.789075 CGACGTTCGATGGCGGGT 62.789 66.667 5.57 0.00 43.74 5.28
5524 11421 2.252260 CTTTGTGCCAGCGGTTCG 59.748 61.111 0.00 0.00 0.00 3.95
5590 11489 1.764723 TCATGGTCATGGCTGTAGGAG 59.235 52.381 10.61 0.00 39.24 3.69
5614 11513 1.953138 GAGATCCAGCGGCGATGTG 60.953 63.158 24.41 15.17 0.00 3.21
5635 11534 1.283347 TCTCTCTCCCATTGCAGCTT 58.717 50.000 0.00 0.00 0.00 3.74
5645 11544 1.448717 GCTTGGCGTTCTCTCTCCC 60.449 63.158 0.00 0.00 0.00 4.30
5647 11546 1.357991 GCAGCTTGGCGTTCTCTCTC 61.358 60.000 0.00 0.00 0.00 3.20
5670 11569 2.362503 AGATCTGGTGTCGGGCGA 60.363 61.111 0.00 0.00 0.00 5.54
5700 11599 2.275418 GTCCACGGCCATGGGAAT 59.725 61.111 19.74 0.00 40.49 3.01
5702 11601 3.716195 CTGTCCACGGCCATGGGA 61.716 66.667 19.74 10.69 40.49 4.37
5724 11623 1.144716 CATGAGCTTCTAGGCGGCA 59.855 57.895 13.08 0.00 37.29 5.69
5725 11624 1.596477 CCATGAGCTTCTAGGCGGC 60.596 63.158 0.00 0.00 37.29 6.53
5769 11691 1.830847 AACCGGTGGAGTTTTGGGC 60.831 57.895 8.52 0.00 0.00 5.36
5784 11706 3.050275 GCTGTCTCCCGTGCAACC 61.050 66.667 0.00 0.00 0.00 3.77
5785 11707 3.050275 GGCTGTCTCCCGTGCAAC 61.050 66.667 0.00 0.00 0.00 4.17
5792 11714 3.462678 GTCCTCCGGCTGTCTCCC 61.463 72.222 0.00 0.00 0.00 4.30
5866 11794 1.507141 GCCACAGGAACAACCACTCG 61.507 60.000 0.00 0.00 42.04 4.18
5880 11808 0.252513 TCTAACCCTAGCCAGCCACA 60.253 55.000 0.00 0.00 0.00 4.17
5882 11810 0.909623 GTTCTAACCCTAGCCAGCCA 59.090 55.000 0.00 0.00 0.00 4.75
5925 11853 3.894547 TTTCCACTTCCTCCGCGCC 62.895 63.158 0.00 0.00 0.00 6.53
5932 11860 3.716872 TCCTTCAGAACTTTCCACTTCCT 59.283 43.478 0.00 0.00 0.00 3.36
5980 11908 4.937201 ACCCTTGGTTTGACTTGAATTC 57.063 40.909 0.00 0.00 27.29 2.17
5999 11927 2.171003 AGCCATTTTTGCTCTGGTACC 58.829 47.619 4.43 4.43 32.41 3.34
6054 11985 2.805099 CTGCCTCGAATTTAGATGCCTC 59.195 50.000 4.79 0.00 0.00 4.70
6063 11994 4.702131 AGAATGTTTAGCTGCCTCGAATTT 59.298 37.500 0.00 0.00 0.00 1.82
6064 11995 4.265073 AGAATGTTTAGCTGCCTCGAATT 58.735 39.130 0.00 0.00 0.00 2.17
6065 11996 3.878778 AGAATGTTTAGCTGCCTCGAAT 58.121 40.909 0.00 0.00 0.00 3.34
6066 11997 3.334583 AGAATGTTTAGCTGCCTCGAA 57.665 42.857 0.00 0.00 0.00 3.71
6067 11998 3.194755 TGTAGAATGTTTAGCTGCCTCGA 59.805 43.478 0.00 0.00 0.00 4.04
6068 11999 3.307242 GTGTAGAATGTTTAGCTGCCTCG 59.693 47.826 0.00 0.00 0.00 4.63
6069 12000 4.508662 AGTGTAGAATGTTTAGCTGCCTC 58.491 43.478 0.00 0.00 0.00 4.70
6070 12001 4.020218 TGAGTGTAGAATGTTTAGCTGCCT 60.020 41.667 0.00 0.00 0.00 4.75
6071 12002 4.253685 TGAGTGTAGAATGTTTAGCTGCC 58.746 43.478 0.00 0.00 0.00 4.85
6072 12003 5.163814 CCTTGAGTGTAGAATGTTTAGCTGC 60.164 44.000 0.00 0.00 0.00 5.25
6073 12004 5.163814 GCCTTGAGTGTAGAATGTTTAGCTG 60.164 44.000 0.00 0.00 0.00 4.24
6074 12005 4.938226 GCCTTGAGTGTAGAATGTTTAGCT 59.062 41.667 0.00 0.00 0.00 3.32
6075 12006 4.695455 TGCCTTGAGTGTAGAATGTTTAGC 59.305 41.667 0.00 0.00 0.00 3.09
6076 12007 6.820656 AGATGCCTTGAGTGTAGAATGTTTAG 59.179 38.462 0.00 0.00 0.00 1.85
6077 12008 6.711277 AGATGCCTTGAGTGTAGAATGTTTA 58.289 36.000 0.00 0.00 0.00 2.01
6078 12009 5.564550 AGATGCCTTGAGTGTAGAATGTTT 58.435 37.500 0.00 0.00 0.00 2.83
6079 12010 5.171339 AGATGCCTTGAGTGTAGAATGTT 57.829 39.130 0.00 0.00 0.00 2.71
6080 12011 4.833478 AGATGCCTTGAGTGTAGAATGT 57.167 40.909 0.00 0.00 0.00 2.71
6081 12012 6.595326 TGTTTAGATGCCTTGAGTGTAGAATG 59.405 38.462 0.00 0.00 0.00 2.67
6082 12013 6.711277 TGTTTAGATGCCTTGAGTGTAGAAT 58.289 36.000 0.00 0.00 0.00 2.40
6083 12014 6.109156 TGTTTAGATGCCTTGAGTGTAGAA 57.891 37.500 0.00 0.00 0.00 2.10
6084 12015 5.738619 TGTTTAGATGCCTTGAGTGTAGA 57.261 39.130 0.00 0.00 0.00 2.59
6085 12016 5.877012 ACATGTTTAGATGCCTTGAGTGTAG 59.123 40.000 0.00 0.00 0.00 2.74
6086 12017 5.804639 ACATGTTTAGATGCCTTGAGTGTA 58.195 37.500 0.00 0.00 0.00 2.90
6087 12018 4.655963 ACATGTTTAGATGCCTTGAGTGT 58.344 39.130 0.00 0.00 0.00 3.55
6088 12019 5.220739 GCTACATGTTTAGATGCCTTGAGTG 60.221 44.000 2.30 0.00 0.00 3.51
6089 12020 4.878397 GCTACATGTTTAGATGCCTTGAGT 59.122 41.667 2.30 0.00 0.00 3.41
6090 12021 4.025396 CGCTACATGTTTAGATGCCTTGAG 60.025 45.833 2.30 0.00 0.00 3.02
6091 12022 3.871006 CGCTACATGTTTAGATGCCTTGA 59.129 43.478 2.30 0.00 0.00 3.02
6092 12023 3.546815 GCGCTACATGTTTAGATGCCTTG 60.547 47.826 2.30 0.00 0.00 3.61
6093 12024 2.614057 GCGCTACATGTTTAGATGCCTT 59.386 45.455 2.30 0.00 0.00 4.35
6094 12025 2.213499 GCGCTACATGTTTAGATGCCT 58.787 47.619 2.30 0.00 0.00 4.75
6095 12026 1.939934 TGCGCTACATGTTTAGATGCC 59.060 47.619 9.73 0.00 0.00 4.40
6096 12027 3.885484 ATGCGCTACATGTTTAGATGC 57.115 42.857 9.73 5.08 37.70 3.91
6097 12028 5.160699 ACAATGCGCTACATGTTTAGATG 57.839 39.130 9.73 0.00 39.60 2.90
6098 12029 6.705825 TCATACAATGCGCTACATGTTTAGAT 59.294 34.615 9.73 0.00 39.60 1.98
6099 12030 6.045955 TCATACAATGCGCTACATGTTTAGA 58.954 36.000 9.73 4.88 39.60 2.10
6100 12031 6.285790 TCATACAATGCGCTACATGTTTAG 57.714 37.500 9.73 0.00 39.60 1.85
6101 12032 6.859420 ATCATACAATGCGCTACATGTTTA 57.141 33.333 9.73 0.00 39.60 2.01
6297 12232 3.668821 TGTATGGATGGTCCCTCTCATT 58.331 45.455 4.35 0.00 35.03 2.57
6304 12239 1.691976 TCGTGATGTATGGATGGTCCC 59.308 52.381 0.00 0.00 35.03 4.46
6307 12242 4.442706 GTTCTTCGTGATGTATGGATGGT 58.557 43.478 0.00 0.00 0.00 3.55
6316 12255 1.800805 CAGCAGGTTCTTCGTGATGT 58.199 50.000 0.00 0.00 41.46 3.06
6407 12346 5.914898 TGACAAGCTACTGCAGTATAGAA 57.085 39.130 26.22 6.56 42.74 2.10
6452 12391 3.186613 GTGCTTTAGTCCACTGCAGTAAC 59.813 47.826 21.20 19.89 34.15 2.50
6462 12401 3.760151 TCTAGCGTTAGTGCTTTAGTCCA 59.240 43.478 6.18 0.00 44.46 4.02
6644 12594 7.441157 TGGACTAACTGAACACTTTGATACAAG 59.559 37.037 0.00 0.00 0.00 3.16
6652 12602 3.131396 CGCTGGACTAACTGAACACTTT 58.869 45.455 0.00 0.00 0.00 2.66
6696 12646 5.443170 CGCAAACAGTTTGTCAAAAGTGAAG 60.443 40.000 23.96 0.00 45.78 3.02
6697 12647 4.384247 CGCAAACAGTTTGTCAAAAGTGAA 59.616 37.500 23.96 0.00 45.78 3.18
6704 12670 2.983136 CACAACGCAAACAGTTTGTCAA 59.017 40.909 23.96 0.00 42.56 3.18
6929 13052 6.916360 TGGAAAAAGGTTCTCTATGCAATT 57.084 33.333 0.00 0.00 0.00 2.32
6958 13081 6.144078 TCCTCCTTTCCGAAAAAGAAAAAG 57.856 37.500 10.67 0.00 33.06 2.27
6960 13083 6.724893 AATCCTCCTTTCCGAAAAAGAAAA 57.275 33.333 10.67 0.00 33.06 2.29
7107 13313 6.604171 TGTCCAAGCCTACATATTCATTCAT 58.396 36.000 0.00 0.00 0.00 2.57
7108 13314 6.000246 TGTCCAAGCCTACATATTCATTCA 58.000 37.500 0.00 0.00 0.00 2.57
7141 13347 6.882610 AAATTCTGCAACTGTGATCTAACA 57.117 33.333 0.00 0.00 0.00 2.41
7152 13358 3.732212 GGCTTTCCAAAATTCTGCAACT 58.268 40.909 0.00 0.00 0.00 3.16
7154 13360 2.363680 TCGGCTTTCCAAAATTCTGCAA 59.636 40.909 0.00 0.00 0.00 4.08
7165 13371 3.695830 ATTAACAGACTCGGCTTTCCA 57.304 42.857 0.00 0.00 0.00 3.53
7174 13380 9.495754 GATTGTAGATGCAAAATTAACAGACTC 57.504 33.333 0.00 0.00 31.63 3.36
7175 13381 9.236006 AGATTGTAGATGCAAAATTAACAGACT 57.764 29.630 0.00 0.00 31.63 3.24
7195 13401 9.654663 GAGACAGGTATTTGTAGTTTAGATTGT 57.345 33.333 0.00 0.00 0.00 2.71
7196 13402 9.653287 TGAGACAGGTATTTGTAGTTTAGATTG 57.347 33.333 0.00 0.00 0.00 2.67
7199 13405 9.871238 GAATGAGACAGGTATTTGTAGTTTAGA 57.129 33.333 0.00 0.00 0.00 2.10
7200 13406 9.653287 TGAATGAGACAGGTATTTGTAGTTTAG 57.347 33.333 0.00 0.00 0.00 1.85
7201 13407 9.653287 CTGAATGAGACAGGTATTTGTAGTTTA 57.347 33.333 0.00 0.00 0.00 2.01
7202 13408 8.375506 TCTGAATGAGACAGGTATTTGTAGTTT 58.624 33.333 0.00 0.00 36.22 2.66
7203 13409 7.907389 TCTGAATGAGACAGGTATTTGTAGTT 58.093 34.615 0.00 0.00 36.22 2.24
7204 13410 7.482169 TCTGAATGAGACAGGTATTTGTAGT 57.518 36.000 0.00 0.00 36.22 2.73
7205 13411 8.420222 AGATCTGAATGAGACAGGTATTTGTAG 58.580 37.037 0.00 0.00 36.22 2.74
7206 13412 8.311395 AGATCTGAATGAGACAGGTATTTGTA 57.689 34.615 0.00 0.00 36.22 2.41
7207 13413 7.192852 AGATCTGAATGAGACAGGTATTTGT 57.807 36.000 0.00 0.00 36.22 2.83
7208 13414 9.775854 ATTAGATCTGAATGAGACAGGTATTTG 57.224 33.333 5.18 0.00 36.22 2.32
7211 13417 9.593565 TGTATTAGATCTGAATGAGACAGGTAT 57.406 33.333 5.18 0.00 36.22 2.73
7212 13418 8.996651 TGTATTAGATCTGAATGAGACAGGTA 57.003 34.615 5.18 0.00 36.22 3.08
7213 13419 7.904558 TGTATTAGATCTGAATGAGACAGGT 57.095 36.000 5.18 0.00 36.22 4.00
7230 13436 6.488006 ACATTCAAGCCTTGCCTATGTATTAG 59.512 38.462 14.07 0.00 30.62 1.73


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

AutoCloner maintained by Alex Coulton.