Multiple sequence alignment - TraesCS7A01G426600

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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 TraesCS7A01G426600 chr7A 100.000 3350 0 0 1 3350 619577768 619574419 0.000000e+00 6187.0
1 TraesCS7A01G426600 chr7A 89.471 1871 106 47 547 2368 619167507 619165679 0.000000e+00 2279.0
2 TraesCS7A01G426600 chr7A 88.469 1561 92 36 862 2365 620171357 620172886 0.000000e+00 1805.0
3 TraesCS7A01G426600 chr7A 89.477 1454 82 31 862 2269 620201263 620202691 0.000000e+00 1772.0
4 TraesCS7A01G426600 chr7A 87.675 1501 124 42 674 2156 619906733 619908190 0.000000e+00 1690.0
5 TraesCS7A01G426600 chr7A 86.100 1518 140 47 674 2163 619634465 619632991 0.000000e+00 1568.0
6 TraesCS7A01G426600 chr7A 89.936 467 24 14 2898 3348 619290333 619289874 6.230000e-162 580.0
7 TraesCS7A01G426600 chr7A 87.160 514 26 15 2818 3310 619165070 619164576 6.320000e-152 547.0
8 TraesCS7A01G426600 chr7A 89.151 424 21 15 2887 3292 620173832 620174248 3.860000e-139 505.0
9 TraesCS7A01G426600 chr7A 81.629 626 50 28 2385 2985 619291201 619290616 3.050000e-125 459.0
10 TraesCS7A01G426600 chr7A 88.981 363 22 3 2382 2728 620172870 620173230 1.850000e-117 433.0
11 TraesCS7A01G426600 chr7A 87.285 291 18 9 2438 2722 619165443 619165166 6.980000e-82 315.0
12 TraesCS7A01G426600 chr7A 85.771 253 34 2 1 252 619167755 619167504 1.980000e-67 267.0
13 TraesCS7A01G426600 chr7A 84.647 241 18 13 3067 3295 620216712 620216945 4.350000e-54 222.0
14 TraesCS7A01G426600 chr7A 88.991 109 2 4 2306 2412 620178764 620178864 3.510000e-25 126.0
15 TraesCS7A01G426600 chr7A 93.443 61 4 0 2385 2445 619165695 619165635 1.280000e-14 91.6
16 TraesCS7A01G426600 chr7D 90.479 1775 92 42 547 2288 538141365 538139635 0.000000e+00 2270.0
17 TraesCS7A01G426600 chr7D 87.718 1490 113 41 828 2268 538661798 538663266 0.000000e+00 1674.0
18 TraesCS7A01G426600 chr7D 87.927 1375 88 36 828 2157 538602389 538603730 0.000000e+00 1548.0
19 TraesCS7A01G426600 chr7D 88.018 1327 96 37 857 2157 538594545 538595834 0.000000e+00 1511.0
20 TraesCS7A01G426600 chr7D 84.645 1029 107 33 674 1686 538585822 538586815 0.000000e+00 977.0
21 TraesCS7A01G426600 chr7D 89.655 609 53 5 1079 1686 538212150 538211551 0.000000e+00 767.0
22 TraesCS7A01G426600 chr7D 84.686 542 35 16 547 1082 538240418 538239919 6.450000e-137 497.0
23 TraesCS7A01G426600 chr7D 89.086 394 22 8 2973 3350 538138970 538138582 1.410000e-128 470.0
24 TraesCS7A01G426600 chr7D 89.961 259 18 3 2727 2985 538139246 538138996 8.960000e-86 327.0
25 TraesCS7A01G426600 chr7D 85.489 317 21 9 2412 2728 538139571 538139280 1.170000e-79 307.0
26 TraesCS7A01G426600 chr7D 84.848 264 34 4 7 270 538240658 538240401 9.220000e-66 261.0
27 TraesCS7A01G426600 chr7D 84.314 255 22 10 3062 3309 538665789 538666032 2.010000e-57 233.0
28 TraesCS7A01G426600 chr7D 93.750 80 5 0 173 252 538141441 538141362 1.630000e-23 121.0
29 TraesCS7A01G426600 chr7D 100.000 30 0 0 2383 2412 538663826 538663855 4.670000e-04 56.5
30 TraesCS7A01G426600 chr7B 88.869 1671 107 34 547 2194 580886190 580884576 0.000000e+00 1982.0
31 TraesCS7A01G426600 chr7B 85.936 1543 131 53 674 2163 580970737 580969228 0.000000e+00 1568.0
32 TraesCS7A01G426600 chr7B 87.821 1322 109 29 857 2163 581313554 581314838 0.000000e+00 1502.0
33 TraesCS7A01G426600 chr7B 90.385 832 45 19 862 1686 581333207 581334010 0.000000e+00 1061.0
34 TraesCS7A01G426600 chr7B 90.826 545 34 7 1726 2268 581334077 581334607 0.000000e+00 715.0
35 TraesCS7A01G426600 chr7B 87.263 581 35 16 2727 3301 580883951 580883404 7.890000e-176 627.0
36 TraesCS7A01G426600 chr7B 98.653 297 4 0 252 548 337593406 337593702 8.230000e-146 527.0
37 TraesCS7A01G426600 chr7B 87.464 351 21 11 2385 2728 580884357 580884023 1.890000e-102 383.0
38 TraesCS7A01G426600 chr7B 89.286 112 8 2 159 270 580886280 580886173 1.620000e-28 137.0
39 TraesCS7A01G426600 chr2B 99.007 302 3 0 249 550 784782135 784782436 2.940000e-150 542.0
40 TraesCS7A01G426600 chr5B 98.013 302 5 1 247 548 375130849 375130549 1.060000e-144 523.0
41 TraesCS7A01G426600 chr6A 98.322 298 4 1 251 547 604571830 604572127 3.830000e-144 521.0
42 TraesCS7A01G426600 chr3A 97.010 301 9 0 252 552 470711337 470711637 1.070000e-139 507.0
43 TraesCS7A01G426600 chr1A 96.633 297 5 3 252 548 543066937 543067228 3.880000e-134 488.0
44 TraesCS7A01G426600 chr1A 82.645 121 21 0 6 126 559935203 559935083 1.270000e-19 108.0
45 TraesCS7A01G426600 chr2A 95.082 305 12 3 248 551 447140277 447139975 8.410000e-131 477.0
46 TraesCS7A01G426600 chr3B 95.033 302 14 1 251 552 500306186 500305886 1.090000e-129 473.0
47 TraesCS7A01G426600 chr2D 94.754 305 12 2 248 551 336960967 336960666 3.910000e-129 472.0


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 TraesCS7A01G426600 chr7A 619574419 619577768 3349 True 6187.000000 6187 100.000000 1 3350 1 chr7A.!!$R1 3349
1 TraesCS7A01G426600 chr7A 620201263 620202691 1428 False 1772.000000 1772 89.477000 862 2269 1 chr7A.!!$F3 1407
2 TraesCS7A01G426600 chr7A 619906733 619908190 1457 False 1690.000000 1690 87.675000 674 2156 1 chr7A.!!$F1 1482
3 TraesCS7A01G426600 chr7A 619632991 619634465 1474 True 1568.000000 1568 86.100000 674 2163 1 chr7A.!!$R2 1489
4 TraesCS7A01G426600 chr7A 620171357 620174248 2891 False 914.333333 1805 88.867000 862 3292 3 chr7A.!!$F5 2430
5 TraesCS7A01G426600 chr7A 619164576 619167755 3179 True 699.920000 2279 88.626000 1 3310 5 chr7A.!!$R3 3309
6 TraesCS7A01G426600 chr7A 619289874 619291201 1327 True 519.500000 580 85.782500 2385 3348 2 chr7A.!!$R4 963
7 TraesCS7A01G426600 chr7D 538602389 538603730 1341 False 1548.000000 1548 87.927000 828 2157 1 chr7D.!!$F3 1329
8 TraesCS7A01G426600 chr7D 538594545 538595834 1289 False 1511.000000 1511 88.018000 857 2157 1 chr7D.!!$F2 1300
9 TraesCS7A01G426600 chr7D 538585822 538586815 993 False 977.000000 977 84.645000 674 1686 1 chr7D.!!$F1 1012
10 TraesCS7A01G426600 chr7D 538211551 538212150 599 True 767.000000 767 89.655000 1079 1686 1 chr7D.!!$R1 607
11 TraesCS7A01G426600 chr7D 538138582 538141441 2859 True 699.000000 2270 89.753000 173 3350 5 chr7D.!!$R2 3177
12 TraesCS7A01G426600 chr7D 538661798 538666032 4234 False 654.500000 1674 90.677333 828 3309 3 chr7D.!!$F4 2481
13 TraesCS7A01G426600 chr7D 538239919 538240658 739 True 379.000000 497 84.767000 7 1082 2 chr7D.!!$R3 1075
14 TraesCS7A01G426600 chr7B 580969228 580970737 1509 True 1568.000000 1568 85.936000 674 2163 1 chr7B.!!$R1 1489
15 TraesCS7A01G426600 chr7B 581313554 581314838 1284 False 1502.000000 1502 87.821000 857 2163 1 chr7B.!!$F2 1306
16 TraesCS7A01G426600 chr7B 581333207 581334607 1400 False 888.000000 1061 90.605500 862 2268 2 chr7B.!!$F3 1406
17 TraesCS7A01G426600 chr7B 580883404 580886280 2876 True 782.250000 1982 88.220500 159 3301 4 chr7B.!!$R2 3142

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
89 90 1.002921 TCCCTGGTCCATGGATCGT 59.997 57.895 19.62 0.0 0.00 3.73 F
259 261 1.132689 CCATCCCTACTTAGGCCTCCT 60.133 57.143 9.68 0.0 42.26 3.69 F
798 807 1.226717 GACAGTCGGGCGTCTCATC 60.227 63.158 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1549 1.343142 CCAAACCAAGTTAGGCAACCC 59.657 52.381 0.00 0.00 35.05 4.11 R
2161 2354 1.456331 GCTTGCTGGGTGGGCATAT 60.456 57.895 0.00 0.00 39.54 1.78 R
2637 4134 1.289109 TTCCTTTGTCGCGCTAGTGC 61.289 55.000 18.49 18.49 0.00 4.40 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
69 70 1.228154 GCTCACCAAAGGGACCGTT 60.228 57.895 0.00 0.00 38.05 4.44
70 71 1.515521 GCTCACCAAAGGGACCGTTG 61.516 60.000 9.63 9.63 38.05 4.10
89 90 1.002921 TCCCTGGTCCATGGATCGT 59.997 57.895 19.62 0.00 0.00 3.73
105 106 4.137872 GTAGCCGCCGTACCAGCA 62.138 66.667 3.68 0.00 0.00 4.41
106 107 3.833645 TAGCCGCCGTACCAGCAG 61.834 66.667 3.68 0.00 0.00 4.24
123 124 4.135153 GCGAGCAGCCGGAGAAGA 62.135 66.667 5.05 0.00 40.81 2.87
126 128 4.140599 AGCAGCCGGAGAAGAGCG 62.141 66.667 5.05 0.00 0.00 5.03
135 137 1.599667 CGGAGAAGAGCGCGCTTATAA 60.600 52.381 36.87 0.00 0.00 0.98
157 159 6.780706 AATTTTATATCACTTAGTCGCCCG 57.219 37.500 0.00 0.00 0.00 6.13
201 203 3.574396 ACGAGGAATCTTCACACTCTTCA 59.426 43.478 0.00 0.00 0.00 3.02
221 223 6.699575 TTCAAGAAGAAGAAAAAGGTGGAG 57.300 37.500 0.00 0.00 0.00 3.86
247 249 2.694616 TGATCGTCCATCCATCCCTA 57.305 50.000 0.00 0.00 0.00 3.53
248 250 2.248248 TGATCGTCCATCCATCCCTAC 58.752 52.381 0.00 0.00 0.00 3.18
249 251 2.158310 TGATCGTCCATCCATCCCTACT 60.158 50.000 0.00 0.00 0.00 2.57
250 252 2.471815 TCGTCCATCCATCCCTACTT 57.528 50.000 0.00 0.00 0.00 2.24
251 253 3.605726 TCGTCCATCCATCCCTACTTA 57.394 47.619 0.00 0.00 0.00 2.24
252 254 3.497332 TCGTCCATCCATCCCTACTTAG 58.503 50.000 0.00 0.00 0.00 2.18
253 255 2.563179 CGTCCATCCATCCCTACTTAGG 59.437 54.545 0.00 0.00 43.25 2.69
254 256 2.303311 GTCCATCCATCCCTACTTAGGC 59.697 54.545 0.00 0.00 42.26 3.93
255 257 1.630878 CCATCCATCCCTACTTAGGCC 59.369 57.143 0.00 0.00 42.26 5.19
256 258 2.625639 CATCCATCCCTACTTAGGCCT 58.374 52.381 11.78 11.78 42.26 5.19
257 259 2.400467 TCCATCCCTACTTAGGCCTC 57.600 55.000 9.68 0.00 42.26 4.70
258 260 1.132817 TCCATCCCTACTTAGGCCTCC 60.133 57.143 9.68 0.00 42.26 4.30
259 261 1.132689 CCATCCCTACTTAGGCCTCCT 60.133 57.143 9.68 0.00 42.26 3.69
260 262 2.695585 CATCCCTACTTAGGCCTCCTT 58.304 52.381 9.68 0.00 42.26 3.36
261 263 2.963654 TCCCTACTTAGGCCTCCTTT 57.036 50.000 9.68 0.00 42.26 3.11
262 264 2.478292 TCCCTACTTAGGCCTCCTTTG 58.522 52.381 9.68 0.00 42.26 2.77
263 265 1.490910 CCCTACTTAGGCCTCCTTTGG 59.509 57.143 9.68 7.86 42.26 3.28
264 266 2.197465 CCTACTTAGGCCTCCTTTGGT 58.803 52.381 9.68 2.89 36.53 3.67
265 267 2.576648 CCTACTTAGGCCTCCTTTGGTT 59.423 50.000 9.68 0.00 36.53 3.67
266 268 2.881111 ACTTAGGCCTCCTTTGGTTC 57.119 50.000 9.68 0.00 34.61 3.62
267 269 2.062636 ACTTAGGCCTCCTTTGGTTCA 58.937 47.619 9.68 0.00 34.61 3.18
268 270 2.649816 ACTTAGGCCTCCTTTGGTTCAT 59.350 45.455 9.68 0.00 34.61 2.57
269 271 3.850173 ACTTAGGCCTCCTTTGGTTCATA 59.150 43.478 9.68 0.00 34.61 2.15
270 272 4.080299 ACTTAGGCCTCCTTTGGTTCATAG 60.080 45.833 9.68 0.00 34.61 2.23
271 273 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
272 274 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
273 275 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
274 276 3.394606 GGCCTCCTTTGGTTCATAGGATA 59.605 47.826 0.00 0.00 39.94 2.59
275 277 4.505742 GGCCTCCTTTGGTTCATAGGATAG 60.506 50.000 0.00 4.66 39.94 2.08
276 278 4.505742 GCCTCCTTTGGTTCATAGGATAGG 60.506 50.000 7.38 7.57 39.94 2.57
277 279 4.907875 CCTCCTTTGGTTCATAGGATAGGA 59.092 45.833 7.38 0.00 39.94 2.94
278 280 5.369699 CCTCCTTTGGTTCATAGGATAGGAA 59.630 44.000 7.38 0.00 39.94 3.36
279 281 6.044871 CCTCCTTTGGTTCATAGGATAGGAAT 59.955 42.308 7.38 0.00 43.72 3.01
280 282 7.237679 CCTCCTTTGGTTCATAGGATAGGAATA 59.762 40.741 7.38 0.00 43.72 1.75
281 283 8.575736 TCCTTTGGTTCATAGGATAGGAATAA 57.424 34.615 3.54 0.00 43.72 1.40
282 284 9.182642 TCCTTTGGTTCATAGGATAGGAATAAT 57.817 33.333 3.54 0.00 43.72 1.28
311 313 9.844257 AGGAATAGGAAAATCATAGAAAGTGAG 57.156 33.333 0.00 0.00 0.00 3.51
312 314 9.838339 GGAATAGGAAAATCATAGAAAGTGAGA 57.162 33.333 0.00 0.00 0.00 3.27
316 318 8.729805 AGGAAAATCATAGAAAGTGAGATGAC 57.270 34.615 0.00 0.00 31.41 3.06
317 319 8.324306 AGGAAAATCATAGAAAGTGAGATGACA 58.676 33.333 0.00 0.00 31.41 3.58
318 320 9.118300 GGAAAATCATAGAAAGTGAGATGACAT 57.882 33.333 0.00 0.00 31.41 3.06
319 321 9.932699 GAAAATCATAGAAAGTGAGATGACATG 57.067 33.333 0.00 0.00 31.41 3.21
320 322 7.493743 AATCATAGAAAGTGAGATGACATGC 57.506 36.000 0.00 0.00 31.41 4.06
321 323 5.981174 TCATAGAAAGTGAGATGACATGCA 58.019 37.500 0.00 0.00 0.00 3.96
322 324 6.589135 TCATAGAAAGTGAGATGACATGCAT 58.411 36.000 0.00 0.00 40.77 3.96
337 339 8.929260 ATGACATGCATCTCAAATCCTATAAA 57.071 30.769 8.81 0.00 28.85 1.40
338 340 8.387190 TGACATGCATCTCAAATCCTATAAAG 57.613 34.615 1.73 0.00 0.00 1.85
339 341 8.212995 TGACATGCATCTCAAATCCTATAAAGA 58.787 33.333 1.73 0.00 0.00 2.52
340 342 8.985315 ACATGCATCTCAAATCCTATAAAGAA 57.015 30.769 0.00 0.00 0.00 2.52
341 343 9.412460 ACATGCATCTCAAATCCTATAAAGAAA 57.588 29.630 0.00 0.00 0.00 2.52
342 344 9.894783 CATGCATCTCAAATCCTATAAAGAAAG 57.105 33.333 0.00 0.00 0.00 2.62
343 345 9.857656 ATGCATCTCAAATCCTATAAAGAAAGA 57.142 29.630 0.00 0.00 0.00 2.52
344 346 9.334947 TGCATCTCAAATCCTATAAAGAAAGAG 57.665 33.333 0.00 0.00 0.00 2.85
345 347 9.553064 GCATCTCAAATCCTATAAAGAAAGAGA 57.447 33.333 0.00 0.00 33.54 3.10
363 365 9.775854 AGAAAGAGATGTCATTTGATGTATAGG 57.224 33.333 0.00 0.00 0.00 2.57
364 366 9.770097 GAAAGAGATGTCATTTGATGTATAGGA 57.230 33.333 0.00 0.00 0.00 2.94
368 370 9.814899 GAGATGTCATTTGATGTATAGGATAGG 57.185 37.037 0.00 0.00 0.00 2.57
369 371 9.552695 AGATGTCATTTGATGTATAGGATAGGA 57.447 33.333 0.00 0.00 0.00 2.94
397 399 9.959721 TTTTTCTATTGAGTCTAGGCTAATGTT 57.040 29.630 0.00 0.00 0.00 2.71
398 400 9.959721 TTTTCTATTGAGTCTAGGCTAATGTTT 57.040 29.630 0.00 0.00 0.00 2.83
399 401 9.959721 TTTCTATTGAGTCTAGGCTAATGTTTT 57.040 29.630 0.00 0.00 0.00 2.43
400 402 9.959721 TTCTATTGAGTCTAGGCTAATGTTTTT 57.040 29.630 0.00 0.00 0.00 1.94
456 458 6.607004 CCTACGTAGGAATAGGAATCCATT 57.393 41.667 33.93 0.00 46.63 3.16
457 459 6.631962 CCTACGTAGGAATAGGAATCCATTC 58.368 44.000 33.93 8.71 46.63 2.67
472 474 7.290110 GAATCCATTCCTATAAACCAAAGGG 57.710 40.000 0.00 0.00 41.29 3.95
473 475 4.542697 TCCATTCCTATAAACCAAAGGGC 58.457 43.478 0.00 0.00 37.90 5.19
474 476 4.231890 TCCATTCCTATAAACCAAAGGGCT 59.768 41.667 0.00 0.00 37.90 5.19
475 477 4.962362 CCATTCCTATAAACCAAAGGGCTT 59.038 41.667 0.00 0.00 37.90 4.35
476 478 5.069119 CCATTCCTATAAACCAAAGGGCTTC 59.931 44.000 0.00 0.00 37.90 3.86
477 479 4.938575 TCCTATAAACCAAAGGGCTTCA 57.061 40.909 0.00 0.00 37.90 3.02
478 480 5.263872 TCCTATAAACCAAAGGGCTTCAA 57.736 39.130 0.00 0.00 37.90 2.69
479 481 5.646215 TCCTATAAACCAAAGGGCTTCAAA 58.354 37.500 0.00 0.00 37.90 2.69
480 482 5.714806 TCCTATAAACCAAAGGGCTTCAAAG 59.285 40.000 0.00 0.00 37.90 2.77
481 483 4.890158 ATAAACCAAAGGGCTTCAAAGG 57.110 40.909 0.00 0.00 37.90 3.11
482 484 2.470057 AACCAAAGGGCTTCAAAGGA 57.530 45.000 0.00 0.00 37.90 3.36
483 485 2.470057 ACCAAAGGGCTTCAAAGGAA 57.530 45.000 0.00 0.00 37.90 3.36
484 486 2.976440 ACCAAAGGGCTTCAAAGGAAT 58.024 42.857 0.00 0.00 37.90 3.01
485 487 3.317406 ACCAAAGGGCTTCAAAGGAATT 58.683 40.909 0.00 0.00 37.90 2.17
486 488 3.716353 ACCAAAGGGCTTCAAAGGAATTT 59.284 39.130 0.00 0.00 37.90 1.82
487 489 4.165950 ACCAAAGGGCTTCAAAGGAATTTT 59.834 37.500 0.00 0.00 37.90 1.82
488 490 5.132502 CCAAAGGGCTTCAAAGGAATTTTT 58.867 37.500 0.00 0.00 31.34 1.94
489 491 5.239306 CCAAAGGGCTTCAAAGGAATTTTTC 59.761 40.000 0.00 0.00 31.34 2.29
490 492 9.962289 ACCAAAGGGCTTCAAAGGAATTTTTCC 62.962 40.741 0.00 0.00 44.02 3.13
507 509 9.121658 GAATTTTTCCTACGAAATTCCTATCCT 57.878 33.333 9.32 0.00 42.34 3.24
508 510 9.475620 AATTTTTCCTACGAAATTCCTATCCTT 57.524 29.630 0.00 0.00 37.81 3.36
509 511 8.873186 TTTTTCCTACGAAATTCCTATCCTTT 57.127 30.769 0.00 0.00 37.81 3.11
510 512 7.859325 TTTCCTACGAAATTCCTATCCTTTG 57.141 36.000 0.00 0.00 32.96 2.77
511 513 5.365619 TCCTACGAAATTCCTATCCTTTGC 58.634 41.667 0.00 0.00 0.00 3.68
512 514 5.104693 TCCTACGAAATTCCTATCCTTTGCA 60.105 40.000 0.00 0.00 0.00 4.08
513 515 5.588648 CCTACGAAATTCCTATCCTTTGCAA 59.411 40.000 0.00 0.00 0.00 4.08
514 516 6.263168 CCTACGAAATTCCTATCCTTTGCAAT 59.737 38.462 0.00 0.00 0.00 3.56
515 517 6.530019 ACGAAATTCCTATCCTTTGCAATT 57.470 33.333 0.00 0.00 0.00 2.32
516 518 6.564328 ACGAAATTCCTATCCTTTGCAATTC 58.436 36.000 0.00 0.00 0.00 2.17
517 519 5.979517 CGAAATTCCTATCCTTTGCAATTCC 59.020 40.000 0.00 0.00 0.00 3.01
518 520 6.183360 CGAAATTCCTATCCTTTGCAATTCCT 60.183 38.462 0.00 0.00 0.00 3.36
519 521 7.013274 CGAAATTCCTATCCTTTGCAATTCCTA 59.987 37.037 0.00 0.00 0.00 2.94
520 522 7.588497 AATTCCTATCCTTTGCAATTCCTAC 57.412 36.000 0.00 0.00 0.00 3.18
521 523 5.708736 TCCTATCCTTTGCAATTCCTACA 57.291 39.130 0.00 0.00 0.00 2.74
522 524 6.073447 TCCTATCCTTTGCAATTCCTACAA 57.927 37.500 0.00 0.00 0.00 2.41
523 525 6.672593 TCCTATCCTTTGCAATTCCTACAAT 58.327 36.000 0.00 0.00 0.00 2.71
524 526 7.811282 TCCTATCCTTTGCAATTCCTACAATA 58.189 34.615 0.00 0.00 0.00 1.90
525 527 8.448008 TCCTATCCTTTGCAATTCCTACAATAT 58.552 33.333 0.00 0.00 0.00 1.28
526 528 9.082313 CCTATCCTTTGCAATTCCTACAATATT 57.918 33.333 0.00 0.00 0.00 1.28
528 530 7.346751 TCCTTTGCAATTCCTACAATATTCC 57.653 36.000 0.00 0.00 0.00 3.01
529 531 7.125391 TCCTTTGCAATTCCTACAATATTCCT 58.875 34.615 0.00 0.00 0.00 3.36
530 532 8.278639 TCCTTTGCAATTCCTACAATATTCCTA 58.721 33.333 0.00 0.00 0.00 2.94
531 533 9.082313 CCTTTGCAATTCCTACAATATTCCTAT 57.918 33.333 0.00 0.00 0.00 2.57
532 534 9.903682 CTTTGCAATTCCTACAATATTCCTATG 57.096 33.333 0.00 0.00 0.00 2.23
533 535 9.639563 TTTGCAATTCCTACAATATTCCTATGA 57.360 29.630 0.00 0.00 0.00 2.15
534 536 9.639563 TTGCAATTCCTACAATATTCCTATGAA 57.360 29.630 0.00 0.00 34.33 2.57
535 537 9.066892 TGCAATTCCTACAATATTCCTATGAAC 57.933 33.333 0.00 0.00 32.13 3.18
536 538 8.515414 GCAATTCCTACAATATTCCTATGAACC 58.485 37.037 0.00 0.00 32.13 3.62
537 539 9.573166 CAATTCCTACAATATTCCTATGAACCA 57.427 33.333 0.00 0.00 32.13 3.67
540 542 9.627123 TTCCTACAATATTCCTATGAACCAAAG 57.373 33.333 0.00 0.00 32.13 2.77
541 543 8.217799 TCCTACAATATTCCTATGAACCAAAGG 58.782 37.037 0.00 0.00 32.13 3.11
542 544 8.217799 CCTACAATATTCCTATGAACCAAAGGA 58.782 37.037 0.00 0.00 37.64 3.36
543 545 9.277783 CTACAATATTCCTATGAACCAAAGGAG 57.722 37.037 0.00 0.00 40.43 3.69
544 546 7.062957 ACAATATTCCTATGAACCAAAGGAGG 58.937 38.462 0.00 0.00 40.43 4.30
545 547 3.366052 TTCCTATGAACCAAAGGAGGC 57.634 47.619 0.00 0.00 40.43 4.70
562 564 4.706962 AGGAGGCCTTATTCATTTGTTCAC 59.293 41.667 6.77 0.00 0.00 3.18
580 582 7.433708 TGTTCACACATTATGTAGTTCCTTG 57.566 36.000 0.00 0.00 40.64 3.61
587 590 9.787435 ACACATTATGTAGTTCCTTGTCTTTTA 57.213 29.630 0.00 0.00 40.88 1.52
719 722 3.664537 GCCGCTAGAAATTTGCTATACGC 60.665 47.826 0.00 0.00 39.77 4.42
721 724 3.120649 CGCTAGAAATTTGCTATACGCCC 60.121 47.826 0.00 0.00 38.05 6.13
798 807 1.226717 GACAGTCGGGCGTCTCATC 60.227 63.158 0.00 0.00 0.00 2.92
1010 1083 1.735018 CGTTCCACTCACACAAACACA 59.265 47.619 0.00 0.00 0.00 3.72
1063 1160 5.591067 TCAACCTTCTTCTAGCTAGCTAGTC 59.409 44.000 38.27 13.74 44.59 2.59
1064 1161 4.466827 ACCTTCTTCTAGCTAGCTAGTCC 58.533 47.826 38.27 6.45 44.59 3.85
1283 1393 2.982130 CTCCGGGTTCCAGTCCAG 59.018 66.667 0.00 0.00 0.00 3.86
1381 1492 6.088616 CGCCTACTACGTAATTAAGCCAATAC 59.911 42.308 0.00 0.00 0.00 1.89
1403 1514 4.128643 CTCATTCATTCCTCTGCTTCTCC 58.871 47.826 0.00 0.00 0.00 3.71
1413 1541 1.478510 TCTGCTTCTCCGTCTTGATCC 59.521 52.381 0.00 0.00 0.00 3.36
1421 1549 3.118992 TCTCCGTCTTGATCCAATGACAG 60.119 47.826 0.00 0.00 0.00 3.51
1714 1891 2.463752 TGTAGGTACATGGACTGACCC 58.536 52.381 8.27 0.00 38.00 4.46
1745 1929 3.694072 GGTGGTGTGAATAATGCAGCTTA 59.306 43.478 0.00 0.00 0.00 3.09
2161 2354 1.616327 AGTGCTCCATGTAGCCCCA 60.616 57.895 7.92 0.00 42.05 4.96
2166 2359 1.952367 GCTCCATGTAGCCCCATATGC 60.952 57.143 0.00 0.00 36.45 3.14
2189 2383 0.682209 CCCAGCAAGCTAGCATTGGT 60.682 55.000 18.83 19.12 38.84 3.67
2269 2490 6.575244 ATGATAAATAAGGACTGGTGTGGA 57.425 37.500 0.00 0.00 0.00 4.02
2271 2492 5.487488 TGATAAATAAGGACTGGTGTGGAGT 59.513 40.000 0.00 0.00 0.00 3.85
2291 2512 6.765989 TGGAGTATAATGTGAAATGTAGCCAC 59.234 38.462 0.00 0.00 0.00 5.01
2292 2513 6.073765 GGAGTATAATGTGAAATGTAGCCACG 60.074 42.308 0.00 0.00 33.78 4.94
2294 2515 5.734855 ATAATGTGAAATGTAGCCACGTC 57.265 39.130 0.00 0.00 33.78 4.34
2295 2516 2.831685 TGTGAAATGTAGCCACGTCT 57.168 45.000 0.00 0.00 33.78 4.18
2296 2517 3.120321 TGTGAAATGTAGCCACGTCTT 57.880 42.857 0.00 0.00 33.78 3.01
2297 2518 3.472652 TGTGAAATGTAGCCACGTCTTT 58.527 40.909 0.00 0.00 33.78 2.52
2299 2520 3.250040 GTGAAATGTAGCCACGTCTTTGT 59.750 43.478 0.00 0.00 0.00 2.83
2300 2521 3.496884 TGAAATGTAGCCACGTCTTTGTC 59.503 43.478 0.00 0.00 0.00 3.18
2301 2522 2.831685 ATGTAGCCACGTCTTTGTCA 57.168 45.000 0.00 0.00 0.00 3.58
2302 2523 1.860676 TGTAGCCACGTCTTTGTCAC 58.139 50.000 0.00 0.00 0.00 3.67
2303 2524 0.782384 GTAGCCACGTCTTTGTCACG 59.218 55.000 0.00 0.00 43.13 4.35
2304 2525 0.942410 TAGCCACGTCTTTGTCACGC 60.942 55.000 0.00 0.00 41.10 5.34
2323 2572 1.612469 CTCACGCTCACGCTCACTTG 61.612 60.000 0.00 0.00 45.53 3.16
2342 2601 6.054941 CACTTGGTGTGTAATATATGCCTCA 58.945 40.000 0.00 0.00 41.53 3.86
2361 3101 5.182760 GCCTCATCTTGTTCTTCTTCATGTT 59.817 40.000 0.00 0.00 0.00 2.71
2362 3102 6.294397 GCCTCATCTTGTTCTTCTTCATGTTT 60.294 38.462 0.00 0.00 0.00 2.83
2363 3103 7.655490 CCTCATCTTGTTCTTCTTCATGTTTT 58.345 34.615 0.00 0.00 0.00 2.43
2364 3104 8.139989 CCTCATCTTGTTCTTCTTCATGTTTTT 58.860 33.333 0.00 0.00 0.00 1.94
2436 3375 0.671251 CTTTGCAACGGCTTGGGTAA 59.329 50.000 0.00 0.00 41.91 2.85
2448 3387 3.571571 GCTTGGGTAAATTGTTCGTTCC 58.428 45.455 0.00 0.00 0.00 3.62
2515 3458 2.464682 GCCAGCAGCTGTTACTCAG 58.535 57.895 21.26 4.98 46.12 3.35
2532 3475 5.700402 ACTCAGTGATATACCTTTGCCTT 57.300 39.130 0.00 0.00 0.00 4.35
2555 3537 1.001974 CAATCAGTCACTCGGGTGGAA 59.998 52.381 17.03 0.00 43.17 3.53
2657 4158 1.359848 CACTAGCGCGACAAAGGAAT 58.640 50.000 12.10 0.00 0.00 3.01
2729 4237 2.614581 GCTAGCTAGCTGCATGTGG 58.385 57.895 33.71 2.77 45.62 4.17
2837 4478 1.098050 GCATTTGACAGGCCACTAGG 58.902 55.000 5.01 0.00 38.23 3.02
2848 4489 0.460459 GCCACTAGGGTTCGCTTCTC 60.460 60.000 0.00 0.00 39.65 2.87
2935 4757 3.380995 TCGTGCTGACATGAGGCT 58.619 55.556 0.00 0.00 36.89 4.58
3016 5544 2.770164 TCCTTTTCCAGAGCTACTGC 57.230 50.000 7.44 0.00 44.52 4.40
3033 5786 6.371825 AGCTACTGCACTGTATTTTTCTTACC 59.628 38.462 0.00 0.00 42.74 2.85
3105 6063 4.890088 TGACGGAGCTTAATTGTTGTACT 58.110 39.130 0.00 0.00 0.00 2.73
3106 6064 6.028146 TGACGGAGCTTAATTGTTGTACTA 57.972 37.500 0.00 0.00 0.00 1.82
3107 6065 5.865552 TGACGGAGCTTAATTGTTGTACTAC 59.134 40.000 0.05 0.05 0.00 2.73
3110 6068 5.004156 CGGAGCTTAATTGTTGTACTACGTC 59.996 44.000 0.00 0.00 0.00 4.34
3113 6071 4.491441 GCTTAATTGTTGTACTACGTCGCC 60.491 45.833 0.00 0.00 0.00 5.54
3176 6137 4.286808 TGATTCATGAACTCTGGACAAGGA 59.713 41.667 11.07 0.00 0.00 3.36
3230 6203 3.868619 TTTAGGTGGGGTATATGCACC 57.131 47.619 4.91 4.91 37.91 5.01
3327 6303 3.528370 CGCAGGACCTCCCTACCG 61.528 72.222 0.00 0.00 45.60 4.02
3335 6311 0.974383 ACCTCCCTACCGTTTCACAG 59.026 55.000 0.00 0.00 0.00 3.66
3342 6318 2.220133 CCTACCGTTTCACAGTTGAACG 59.780 50.000 10.05 10.05 41.64 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.228154 AACGGTCCCTTTGGTGAGC 60.228 57.895 0.00 0.00 0.00 4.26
77 78 1.664965 GCGGCTACGATCCATGGAC 60.665 63.158 18.99 10.34 44.60 4.02
105 106 4.140599 CTTCTCCGGCTGCTCGCT 62.141 66.667 0.00 0.00 39.13 4.93
106 107 4.135153 TCTTCTCCGGCTGCTCGC 62.135 66.667 0.00 0.00 38.13 5.03
123 124 7.596749 AGTGATATAAAATTATAAGCGCGCT 57.403 32.000 31.32 31.32 0.00 5.92
135 137 6.092955 TCGGGCGACTAAGTGATATAAAAT 57.907 37.500 0.00 0.00 0.00 1.82
157 159 8.996988 TCGTATGTTACATTTGTTTGTCTTTC 57.003 30.769 2.23 0.00 0.00 2.62
201 203 6.663734 TCTTCTCCACCTTTTTCTTCTTCTT 58.336 36.000 0.00 0.00 0.00 2.52
221 223 4.453819 GGATGGATGGACGATCAATTCTTC 59.546 45.833 0.00 0.00 35.83 2.87
247 249 2.062636 TGAACCAAAGGAGGCCTAAGT 58.937 47.619 4.42 0.00 31.13 2.24
248 250 2.879103 TGAACCAAAGGAGGCCTAAG 57.121 50.000 4.42 0.00 31.13 2.18
249 251 3.202151 CCTATGAACCAAAGGAGGCCTAA 59.798 47.826 4.42 0.00 31.13 2.69
250 252 2.777692 CCTATGAACCAAAGGAGGCCTA 59.222 50.000 4.42 0.00 31.13 3.93
251 253 1.566231 CCTATGAACCAAAGGAGGCCT 59.434 52.381 3.86 3.86 33.87 5.19
252 254 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
253 255 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
254 256 4.907875 TCCTATCCTATGAACCAAAGGAGG 59.092 45.833 0.00 0.00 42.53 4.30
255 257 6.500589 TTCCTATCCTATGAACCAAAGGAG 57.499 41.667 0.00 0.00 42.53 3.69
256 258 8.575736 TTATTCCTATCCTATGAACCAAAGGA 57.424 34.615 0.00 0.00 43.38 3.36
285 287 9.844257 CTCACTTTCTATGATTTTCCTATTCCT 57.156 33.333 0.00 0.00 0.00 3.36
286 288 9.838339 TCTCACTTTCTATGATTTTCCTATTCC 57.162 33.333 0.00 0.00 0.00 3.01
290 292 9.823647 GTCATCTCACTTTCTATGATTTTCCTA 57.176 33.333 0.00 0.00 31.49 2.94
291 293 8.324306 TGTCATCTCACTTTCTATGATTTTCCT 58.676 33.333 0.00 0.00 31.49 3.36
292 294 8.498054 TGTCATCTCACTTTCTATGATTTTCC 57.502 34.615 0.00 0.00 31.49 3.13
293 295 9.932699 CATGTCATCTCACTTTCTATGATTTTC 57.067 33.333 0.00 0.00 31.49 2.29
294 296 8.404000 GCATGTCATCTCACTTTCTATGATTTT 58.596 33.333 0.00 0.00 31.49 1.82
295 297 7.555195 TGCATGTCATCTCACTTTCTATGATTT 59.445 33.333 0.00 0.00 31.49 2.17
296 298 7.052248 TGCATGTCATCTCACTTTCTATGATT 58.948 34.615 0.00 0.00 31.49 2.57
297 299 6.589135 TGCATGTCATCTCACTTTCTATGAT 58.411 36.000 0.00 0.00 31.49 2.45
298 300 5.981174 TGCATGTCATCTCACTTTCTATGA 58.019 37.500 0.00 0.00 0.00 2.15
299 301 6.862711 ATGCATGTCATCTCACTTTCTATG 57.137 37.500 0.00 0.00 0.00 2.23
312 314 8.929260 TTTATAGGATTTGAGATGCATGTCAT 57.071 30.769 25.41 13.07 38.32 3.06
313 315 8.212995 TCTTTATAGGATTTGAGATGCATGTCA 58.787 33.333 21.70 21.70 0.00 3.58
314 316 8.613060 TCTTTATAGGATTTGAGATGCATGTC 57.387 34.615 16.63 16.63 0.00 3.06
315 317 8.985315 TTCTTTATAGGATTTGAGATGCATGT 57.015 30.769 2.46 0.00 0.00 3.21
316 318 9.894783 CTTTCTTTATAGGATTTGAGATGCATG 57.105 33.333 2.46 0.00 0.00 4.06
317 319 9.857656 TCTTTCTTTATAGGATTTGAGATGCAT 57.142 29.630 0.00 0.00 0.00 3.96
318 320 9.334947 CTCTTTCTTTATAGGATTTGAGATGCA 57.665 33.333 0.00 0.00 0.00 3.96
319 321 9.553064 TCTCTTTCTTTATAGGATTTGAGATGC 57.447 33.333 0.00 0.00 0.00 3.91
337 339 9.775854 CCTATACATCAAATGACATCTCTTTCT 57.224 33.333 0.00 0.00 0.00 2.52
338 340 9.770097 TCCTATACATCAAATGACATCTCTTTC 57.230 33.333 0.00 0.00 0.00 2.62
342 344 9.814899 CCTATCCTATACATCAAATGACATCTC 57.185 37.037 0.00 0.00 0.00 2.75
343 345 9.552695 TCCTATCCTATACATCAAATGACATCT 57.447 33.333 0.00 0.00 0.00 2.90
371 373 9.959721 AACATTAGCCTAGACTCAATAGAAAAA 57.040 29.630 0.00 0.00 0.00 1.94
372 374 9.959721 AAACATTAGCCTAGACTCAATAGAAAA 57.040 29.630 0.00 0.00 0.00 2.29
373 375 9.959721 AAAACATTAGCCTAGACTCAATAGAAA 57.040 29.630 0.00 0.00 0.00 2.52
374 376 9.959721 AAAAACATTAGCCTAGACTCAATAGAA 57.040 29.630 0.00 0.00 0.00 2.10
433 435 6.607004 AATGGATTCCTATTCCTACGTAGG 57.393 41.667 32.05 32.05 45.02 3.18
448 450 6.239317 GCCCTTTGGTTTATAGGAATGGATTC 60.239 42.308 0.00 0.00 36.08 2.52
449 451 5.602561 GCCCTTTGGTTTATAGGAATGGATT 59.397 40.000 0.00 0.00 0.00 3.01
450 452 5.103086 AGCCCTTTGGTTTATAGGAATGGAT 60.103 40.000 0.00 0.00 0.00 3.41
451 453 4.231890 AGCCCTTTGGTTTATAGGAATGGA 59.768 41.667 0.00 0.00 0.00 3.41
452 454 4.546674 AGCCCTTTGGTTTATAGGAATGG 58.453 43.478 0.00 0.00 0.00 3.16
453 455 5.656416 TGAAGCCCTTTGGTTTATAGGAATG 59.344 40.000 0.00 0.00 34.87 2.67
454 456 5.837829 TGAAGCCCTTTGGTTTATAGGAAT 58.162 37.500 0.00 0.00 34.87 3.01
455 457 5.263872 TGAAGCCCTTTGGTTTATAGGAA 57.736 39.130 0.00 0.00 34.87 3.36
456 458 4.938575 TGAAGCCCTTTGGTTTATAGGA 57.061 40.909 0.00 0.00 34.87 2.94
457 459 5.105351 CCTTTGAAGCCCTTTGGTTTATAGG 60.105 44.000 0.00 0.00 34.87 2.57
458 460 5.714806 TCCTTTGAAGCCCTTTGGTTTATAG 59.285 40.000 0.00 0.00 34.87 1.31
459 461 5.646215 TCCTTTGAAGCCCTTTGGTTTATA 58.354 37.500 0.00 0.00 34.87 0.98
460 462 4.488770 TCCTTTGAAGCCCTTTGGTTTAT 58.511 39.130 0.00 0.00 34.87 1.40
461 463 3.917300 TCCTTTGAAGCCCTTTGGTTTA 58.083 40.909 0.00 0.00 34.87 2.01
462 464 2.758130 TCCTTTGAAGCCCTTTGGTTT 58.242 42.857 0.00 0.00 37.85 3.27
463 465 2.470057 TCCTTTGAAGCCCTTTGGTT 57.530 45.000 0.00 0.00 37.39 3.67
464 466 2.470057 TTCCTTTGAAGCCCTTTGGT 57.530 45.000 0.00 0.00 0.00 3.67
465 467 4.356405 AAATTCCTTTGAAGCCCTTTGG 57.644 40.909 0.00 0.00 33.05 3.28
466 468 5.239306 GGAAAAATTCCTTTGAAGCCCTTTG 59.761 40.000 1.86 0.00 46.57 2.77
467 469 5.376625 GGAAAAATTCCTTTGAAGCCCTTT 58.623 37.500 1.86 0.00 46.57 3.11
468 470 4.973168 GGAAAAATTCCTTTGAAGCCCTT 58.027 39.130 1.86 0.00 46.57 3.95
469 471 4.623932 GGAAAAATTCCTTTGAAGCCCT 57.376 40.909 1.86 0.00 46.57 5.19
481 483 9.121658 AGGATAGGAATTTCGTAGGAAAAATTC 57.878 33.333 14.07 13.22 44.76 2.17
482 484 9.475620 AAGGATAGGAATTTCGTAGGAAAAATT 57.524 29.630 14.07 5.69 44.76 1.82
483 485 9.475620 AAAGGATAGGAATTTCGTAGGAAAAAT 57.524 29.630 14.07 6.93 44.76 1.82
484 486 8.736244 CAAAGGATAGGAATTTCGTAGGAAAAA 58.264 33.333 14.07 0.00 44.76 1.94
485 487 7.148137 GCAAAGGATAGGAATTTCGTAGGAAAA 60.148 37.037 14.07 0.00 44.76 2.29
486 488 6.317893 GCAAAGGATAGGAATTTCGTAGGAAA 59.682 38.462 12.62 12.62 45.60 3.13
487 489 5.820947 GCAAAGGATAGGAATTTCGTAGGAA 59.179 40.000 5.21 0.00 0.00 3.36
488 490 5.104693 TGCAAAGGATAGGAATTTCGTAGGA 60.105 40.000 5.21 0.00 0.00 2.94
489 491 5.123227 TGCAAAGGATAGGAATTTCGTAGG 58.877 41.667 5.21 0.00 0.00 3.18
490 492 6.677781 TTGCAAAGGATAGGAATTTCGTAG 57.322 37.500 0.00 0.00 0.00 3.51
491 493 7.201785 GGAATTGCAAAGGATAGGAATTTCGTA 60.202 37.037 1.71 1.61 36.18 3.43
492 494 6.405842 GGAATTGCAAAGGATAGGAATTTCGT 60.406 38.462 1.71 0.00 36.18 3.85
493 495 5.979517 GGAATTGCAAAGGATAGGAATTTCG 59.020 40.000 1.71 0.00 36.18 3.46
494 496 7.117285 AGGAATTGCAAAGGATAGGAATTTC 57.883 36.000 1.71 0.00 36.18 2.17
495 497 7.619302 TGTAGGAATTGCAAAGGATAGGAATTT 59.381 33.333 1.71 0.00 36.18 1.82
496 498 7.125391 TGTAGGAATTGCAAAGGATAGGAATT 58.875 34.615 1.71 0.00 38.28 2.17
497 499 6.672593 TGTAGGAATTGCAAAGGATAGGAAT 58.327 36.000 1.71 0.00 0.00 3.01
498 500 6.073447 TGTAGGAATTGCAAAGGATAGGAA 57.927 37.500 1.71 0.00 0.00 3.36
499 501 5.708736 TGTAGGAATTGCAAAGGATAGGA 57.291 39.130 1.71 0.00 0.00 2.94
500 502 6.966534 ATTGTAGGAATTGCAAAGGATAGG 57.033 37.500 1.71 0.00 34.97 2.57
502 504 9.077885 GGAATATTGTAGGAATTGCAAAGGATA 57.922 33.333 1.71 0.00 34.97 2.59
503 505 7.786464 AGGAATATTGTAGGAATTGCAAAGGAT 59.214 33.333 1.71 0.00 34.97 3.24
504 506 7.125391 AGGAATATTGTAGGAATTGCAAAGGA 58.875 34.615 1.71 0.00 34.97 3.36
505 507 7.352079 AGGAATATTGTAGGAATTGCAAAGG 57.648 36.000 1.71 0.00 34.97 3.11
506 508 9.903682 CATAGGAATATTGTAGGAATTGCAAAG 57.096 33.333 1.71 0.00 34.97 2.77
507 509 9.639563 TCATAGGAATATTGTAGGAATTGCAAA 57.360 29.630 1.71 0.00 34.97 3.68
508 510 9.639563 TTCATAGGAATATTGTAGGAATTGCAA 57.360 29.630 0.00 0.00 35.80 4.08
509 511 9.066892 GTTCATAGGAATATTGTAGGAATTGCA 57.933 33.333 0.00 0.00 35.05 4.08
510 512 8.515414 GGTTCATAGGAATATTGTAGGAATTGC 58.485 37.037 0.00 0.00 35.05 3.56
511 513 9.573166 TGGTTCATAGGAATATTGTAGGAATTG 57.427 33.333 0.00 0.00 35.05 2.32
514 516 9.627123 CTTTGGTTCATAGGAATATTGTAGGAA 57.373 33.333 0.00 0.00 35.05 3.36
515 517 8.217799 CCTTTGGTTCATAGGAATATTGTAGGA 58.782 37.037 0.00 0.00 35.14 2.94
516 518 8.217799 TCCTTTGGTTCATAGGAATATTGTAGG 58.782 37.037 4.94 0.00 38.33 3.18
517 519 9.277783 CTCCTTTGGTTCATAGGAATATTGTAG 57.722 37.037 8.11 0.00 40.12 2.74
518 520 8.217799 CCTCCTTTGGTTCATAGGAATATTGTA 58.782 37.037 8.11 0.00 40.12 2.41
519 521 7.062957 CCTCCTTTGGTTCATAGGAATATTGT 58.937 38.462 8.11 0.00 40.12 2.71
520 522 6.015940 GCCTCCTTTGGTTCATAGGAATATTG 60.016 42.308 8.11 0.00 40.12 1.90
521 523 6.071320 GCCTCCTTTGGTTCATAGGAATATT 58.929 40.000 8.11 0.00 40.12 1.28
522 524 5.458215 GGCCTCCTTTGGTTCATAGGAATAT 60.458 44.000 0.00 0.00 40.12 1.28
523 525 4.141251 GGCCTCCTTTGGTTCATAGGAATA 60.141 45.833 0.00 0.00 40.12 1.75
524 526 3.373110 GGCCTCCTTTGGTTCATAGGAAT 60.373 47.826 0.00 0.00 40.12 3.01
525 527 2.025321 GGCCTCCTTTGGTTCATAGGAA 60.025 50.000 0.00 0.00 40.12 3.36
526 528 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
527 529 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
528 530 3.372440 AAGGCCTCCTTTGGTTCATAG 57.628 47.619 5.23 0.00 41.69 2.23
529 531 5.044476 TGAATAAGGCCTCCTTTGGTTCATA 60.044 40.000 5.23 0.00 41.69 2.15
530 532 4.264352 TGAATAAGGCCTCCTTTGGTTCAT 60.264 41.667 5.23 0.00 41.69 2.57
531 533 3.075283 TGAATAAGGCCTCCTTTGGTTCA 59.925 43.478 5.23 6.51 41.69 3.18
532 534 3.697166 TGAATAAGGCCTCCTTTGGTTC 58.303 45.455 5.23 3.88 41.69 3.62
533 535 3.825908 TGAATAAGGCCTCCTTTGGTT 57.174 42.857 5.23 0.00 41.69 3.67
534 536 4.337264 AATGAATAAGGCCTCCTTTGGT 57.663 40.909 5.23 0.00 41.69 3.67
535 537 4.467438 ACAAATGAATAAGGCCTCCTTTGG 59.533 41.667 5.23 1.15 41.69 3.28
536 538 5.665916 ACAAATGAATAAGGCCTCCTTTG 57.334 39.130 5.23 11.91 41.69 2.77
537 539 5.779771 TGAACAAATGAATAAGGCCTCCTTT 59.220 36.000 5.23 0.00 41.69 3.11
538 540 5.185828 GTGAACAAATGAATAAGGCCTCCTT 59.814 40.000 5.23 1.74 46.63 3.36
539 541 4.706962 GTGAACAAATGAATAAGGCCTCCT 59.293 41.667 5.23 0.00 33.87 3.69
540 542 4.462483 TGTGAACAAATGAATAAGGCCTCC 59.538 41.667 5.23 0.00 0.00 4.30
541 543 5.048083 TGTGTGAACAAATGAATAAGGCCTC 60.048 40.000 5.23 0.00 0.00 4.70
542 544 4.832266 TGTGTGAACAAATGAATAAGGCCT 59.168 37.500 0.00 0.00 0.00 5.19
543 545 5.132897 TGTGTGAACAAATGAATAAGGCC 57.867 39.130 0.00 0.00 0.00 5.19
544 546 8.810427 CATAATGTGTGAACAAATGAATAAGGC 58.190 33.333 0.00 0.00 0.00 4.35
545 547 9.859427 ACATAATGTGTGAACAAATGAATAAGG 57.141 29.630 9.99 0.00 40.28 2.69
580 582 7.812648 TGTACACAAATGGCAGTATAAAAGAC 58.187 34.615 0.00 0.00 0.00 3.01
587 590 6.398234 TGTTTTGTACACAAATGGCAGTAT 57.602 33.333 8.27 0.00 44.30 2.12
719 722 3.490348 AGCCATTAAGAATCGATTGGGG 58.510 45.455 16.96 8.42 0.00 4.96
721 724 5.505173 ACAAGCCATTAAGAATCGATTGG 57.495 39.130 16.96 11.31 0.00 3.16
781 790 1.251527 AAGATGAGACGCCCGACTGT 61.252 55.000 0.00 0.00 0.00 3.55
798 807 3.194968 AGCTGCCAAATTTCTGATGGAAG 59.805 43.478 0.00 0.00 42.04 3.46
1063 1160 2.093106 AGTACGCTCACTCAACTAGGG 58.907 52.381 0.00 0.00 0.00 3.53
1064 1161 3.851976 AAGTACGCTCACTCAACTAGG 57.148 47.619 0.00 0.00 0.00 3.02
1381 1492 4.128643 GGAGAAGCAGAGGAATGAATGAG 58.871 47.826 0.00 0.00 0.00 2.90
1403 1514 2.283298 CCCTGTCATTGGATCAAGACG 58.717 52.381 0.00 0.00 33.83 4.18
1413 1541 2.795329 AGTTAGGCAACCCTGTCATTG 58.205 47.619 0.00 0.00 42.90 2.82
1421 1549 1.343142 CCAAACCAAGTTAGGCAACCC 59.657 52.381 0.00 0.00 35.05 4.11
1695 1855 2.463752 TGGGTCAGTCCATGTACCTAC 58.536 52.381 0.00 0.00 38.11 3.18
1713 1890 1.819928 TCACACCACCAAATCGATGG 58.180 50.000 0.00 0.00 46.38 3.51
1714 1891 5.559427 TTATTCACACCACCAAATCGATG 57.441 39.130 0.00 0.00 0.00 3.84
1745 1929 1.745115 CGGCATGTCGTCCACCATT 60.745 57.895 12.53 0.00 0.00 3.16
1901 2085 2.050934 GTAGGAGGCGGAGAACGGT 61.051 63.158 0.00 0.00 44.51 4.83
2161 2354 1.456331 GCTTGCTGGGTGGGCATAT 60.456 57.895 0.00 0.00 39.54 1.78
2166 2359 2.439156 GCTAGCTTGCTGGGTGGG 60.439 66.667 13.17 0.00 0.00 4.61
2209 2406 1.972660 ATCTTCCCTTTCTCCGGCGG 61.973 60.000 22.51 22.51 0.00 6.13
2269 2490 6.346096 ACGTGGCTACATTTCACATTATACT 58.654 36.000 0.00 0.00 0.00 2.12
2271 2492 6.578944 AGACGTGGCTACATTTCACATTATA 58.421 36.000 0.00 0.00 0.00 0.98
2291 2512 1.482955 CGTGAGCGTGACAAAGACG 59.517 57.895 0.00 0.00 39.87 4.18
2323 2572 6.936900 ACAAGATGAGGCATATATTACACACC 59.063 38.462 0.00 0.00 0.00 4.16
2365 3105 8.768957 TGAAGAACAAACACATGATTCAAAAA 57.231 26.923 0.00 0.00 0.00 1.94
2366 3106 8.819015 CATGAAGAACAAACACATGATTCAAAA 58.181 29.630 0.00 0.00 40.13 2.44
2367 3107 7.980662 ACATGAAGAACAAACACATGATTCAAA 59.019 29.630 0.00 0.00 40.13 2.69
2368 3108 7.435784 CACATGAAGAACAAACACATGATTCAA 59.564 33.333 0.00 0.00 40.13 2.69
2369 3109 6.919115 CACATGAAGAACAAACACATGATTCA 59.081 34.615 0.00 0.00 40.13 2.57
2370 3110 6.919662 ACACATGAAGAACAAACACATGATTC 59.080 34.615 0.00 0.00 40.13 2.52
2371 3111 6.808829 ACACATGAAGAACAAACACATGATT 58.191 32.000 0.00 0.00 40.13 2.57
2372 3112 6.395426 ACACATGAAGAACAAACACATGAT 57.605 33.333 0.00 0.00 40.13 2.45
2373 3113 5.833406 ACACATGAAGAACAAACACATGA 57.167 34.783 0.00 0.00 40.13 3.07
2374 3114 6.310956 ACAAACACATGAAGAACAAACACATG 59.689 34.615 0.00 0.00 42.37 3.21
2375 3115 6.397272 ACAAACACATGAAGAACAAACACAT 58.603 32.000 0.00 0.00 0.00 3.21
2376 3116 5.777802 ACAAACACATGAAGAACAAACACA 58.222 33.333 0.00 0.00 0.00 3.72
2377 3117 6.524490 CAACAAACACATGAAGAACAAACAC 58.476 36.000 0.00 0.00 0.00 3.32
2378 3118 5.119898 GCAACAAACACATGAAGAACAAACA 59.880 36.000 0.00 0.00 0.00 2.83
2379 3119 5.348451 AGCAACAAACACATGAAGAACAAAC 59.652 36.000 0.00 0.00 0.00 2.93
2380 3120 5.477510 AGCAACAAACACATGAAGAACAAA 58.522 33.333 0.00 0.00 0.00 2.83
2381 3121 5.070770 AGCAACAAACACATGAAGAACAA 57.929 34.783 0.00 0.00 0.00 2.83
2382 3122 4.398988 AGAGCAACAAACACATGAAGAACA 59.601 37.500 0.00 0.00 0.00 3.18
2383 3123 4.925068 AGAGCAACAAACACATGAAGAAC 58.075 39.130 0.00 0.00 0.00 3.01
2448 3387 1.349259 GCACACAGTAAGCGTACCGG 61.349 60.000 0.00 0.00 0.00 5.28
2456 3399 5.349817 CAGGATAAGTTGAGCACACAGTAAG 59.650 44.000 0.00 0.00 0.00 2.34
2511 3454 5.431765 ACAAGGCAAAGGTATATCACTGAG 58.568 41.667 0.00 0.00 0.00 3.35
2515 3458 6.318648 TGATTGACAAGGCAAAGGTATATCAC 59.681 38.462 0.00 0.00 0.00 3.06
2532 3475 1.338107 ACCCGAGTGACTGATTGACA 58.662 50.000 0.00 0.00 0.00 3.58
2555 3537 5.239744 CAGCGTAGTCCTATCACTATCAGTT 59.760 44.000 0.00 0.00 31.45 3.16
2637 4134 1.289109 TTCCTTTGTCGCGCTAGTGC 61.289 55.000 18.49 18.49 0.00 4.40
2657 4158 3.773119 GGATTATTACGAGCCCCTATCCA 59.227 47.826 0.00 0.00 32.48 3.41
2837 4478 1.200484 AGACGAGAAGAGAAGCGAACC 59.800 52.381 0.00 0.00 0.00 3.62
2879 4520 2.744202 CAGTTCCTGGACGATGGAAAAG 59.256 50.000 0.00 0.00 43.06 2.27
2880 4521 2.105821 ACAGTTCCTGGACGATGGAAAA 59.894 45.455 0.00 0.00 43.06 2.29
2881 4522 1.697432 ACAGTTCCTGGACGATGGAAA 59.303 47.619 0.00 0.00 43.06 3.13
2935 4757 5.607477 ACGGTACAGAAGAAAATTCAGACA 58.393 37.500 0.00 0.00 0.00 3.41
2971 5499 5.451381 GCAGAAGAATGAAATGCATCATGGA 60.451 40.000 0.00 0.00 39.90 3.41
3033 5786 1.593006 ACGCGACACTCAAGTTGAAAG 59.407 47.619 15.93 4.95 0.00 2.62
3042 5795 0.038618 ATACAAGCACGCGACACTCA 60.039 50.000 15.93 0.00 0.00 3.41
3105 6063 2.292569 GAGTCTATCATTGGGCGACGTA 59.707 50.000 0.00 0.00 0.00 3.57
3106 6064 1.067212 GAGTCTATCATTGGGCGACGT 59.933 52.381 0.00 0.00 0.00 4.34
3107 6065 1.067060 TGAGTCTATCATTGGGCGACG 59.933 52.381 0.00 0.00 31.12 5.12
3110 6068 3.459232 TCTTGAGTCTATCATTGGGCG 57.541 47.619 0.00 0.00 37.89 6.13
3113 6071 6.323482 TCTCCTCTTCTTGAGTCTATCATTGG 59.677 42.308 0.00 0.00 41.11 3.16
3176 6137 4.126520 ACACCCAACCCAATTATGTCTT 57.873 40.909 0.00 0.00 0.00 3.01
3230 6203 0.461516 AGACAGCGTGATGGAGCATG 60.462 55.000 0.00 0.00 35.48 4.06
3327 6303 2.700694 CGGTTCGTTCAACTGTGAAAC 58.299 47.619 0.00 0.00 45.29 2.78


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

AutoCloner maintained by Alex Coulton.