Multiple sequence alignment - TraesCS1D01G127400

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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 TraesCS1D01G127400 chr1D 100.000 3362 0 0 886 4247 139979037 139982398 0.000000e+00 6209.0
1 TraesCS1D01G127400 chr1D 100.000 583 0 0 1 583 139978152 139978734 0.000000e+00 1077.0
2 TraesCS1D01G127400 chr1D 77.457 173 34 3 2748 2916 461506367 461506196 9.720000e-17 99.0
3 TraesCS1D01G127400 chr1D 76.879 173 35 3 2748 2916 461485695 461485524 4.520000e-15 93.5
4 TraesCS1D01G127400 chr1D 100.000 31 0 0 1575 1605 461486743 461486713 1.650000e-04 58.4
5 TraesCS1D01G127400 chr1A 90.898 1692 60 40 886 2526 150902022 150900374 0.000000e+00 2185.0
6 TraesCS1D01G127400 chr1A 89.707 923 40 25 2694 3586 150900027 150899130 0.000000e+00 1127.0
7 TraesCS1D01G127400 chr1A 91.845 699 39 11 3556 4247 150899118 150898431 0.000000e+00 959.0
8 TraesCS1D01G127400 chr1A 92.241 232 17 1 1 232 150902571 150902341 1.140000e-85 327.0
9 TraesCS1D01G127400 chr1A 93.617 47 2 1 2595 2641 435966214 435966259 7.620000e-08 69.4
10 TraesCS1D01G127400 chr1A 100.000 31 0 0 1575 1605 552951600 552951570 1.650000e-04 58.4
11 TraesCS1D01G127400 chr1B 88.201 1017 41 29 1532 2522 198644552 198643589 0.000000e+00 1140.0
12 TraesCS1D01G127400 chr1B 93.624 596 12 8 886 1462 198645173 198644585 0.000000e+00 867.0
13 TraesCS1D01G127400 chr1B 84.406 699 40 40 2662 3322 198643303 198642636 1.300000e-174 623.0
14 TraesCS1D01G127400 chr1B 90.244 246 6 6 1 231 198645903 198645661 5.340000e-79 305.0
15 TraesCS1D01G127400 chr1B 91.304 161 13 1 234 394 648795797 648795956 7.150000e-53 219.0
16 TraesCS1D01G127400 chr1B 92.857 42 1 1 2553 2594 198643397 198643358 4.590000e-05 60.2
17 TraesCS1D01G127400 chr1B 89.362 47 4 1 2595 2641 34206715 34206670 1.650000e-04 58.4
18 TraesCS1D01G127400 chr1B 100.000 31 0 0 1575 1605 634413550 634413520 1.650000e-04 58.4
19 TraesCS1D01G127400 chr1B 100.000 31 0 0 1575 1605 634601333 634601363 1.650000e-04 58.4
20 TraesCS1D01G127400 chrUn 85.065 924 113 20 3333 4247 27217377 27216470 0.000000e+00 918.0
21 TraesCS1D01G127400 chrUn 77.273 176 29 6 2748 2916 218156143 218156314 4.520000e-15 93.5
22 TraesCS1D01G127400 chrUn 77.273 176 29 6 2748 2916 246422226 246422055 4.520000e-15 93.5
23 TraesCS1D01G127400 chr5D 84.740 924 115 21 3333 4247 557520772 557521678 0.000000e+00 902.0
24 TraesCS1D01G127400 chr3B 84.698 928 107 28 3333 4247 782666004 782666909 0.000000e+00 894.0
25 TraesCS1D01G127400 chr3B 88.406 552 39 16 886 1434 826711444 826711973 3.580000e-180 641.0
26 TraesCS1D01G127400 chr3B 92.727 440 30 2 1538 1976 826712094 826712532 5.990000e-178 634.0
27 TraesCS1D01G127400 chr3B 92.780 277 16 3 2692 2965 826712702 826712977 8.560000e-107 398.0
28 TraesCS1D01G127400 chr3B 87.755 49 5 1 2592 2640 794105862 794105909 5.930000e-04 56.5
29 TraesCS1D01G127400 chr2B 84.216 925 120 22 3333 4247 8178859 8179767 0.000000e+00 876.0
30 TraesCS1D01G127400 chr2B 84.279 846 101 26 3412 4247 408302163 408302986 0.000000e+00 797.0
31 TraesCS1D01G127400 chr2B 86.792 53 5 2 2588 2640 8313846 8313896 1.650000e-04 58.4
32 TraesCS1D01G127400 chr4B 82.919 925 132 21 3333 4247 613083520 613084428 0.000000e+00 809.0
33 TraesCS1D01G127400 chr3D 81.937 919 132 29 3337 4244 609280084 609280979 0.000000e+00 747.0
34 TraesCS1D01G127400 chr3D 93.166 439 30 0 1538 1976 612291121 612290683 0.000000e+00 645.0
35 TraesCS1D01G127400 chr3D 88.225 552 39 15 886 1433 612291777 612291248 1.670000e-178 636.0
36 TraesCS1D01G127400 chr3D 90.675 311 19 6 2658 2965 612290594 612290291 5.110000e-109 405.0
37 TraesCS1D01G127400 chr3D 91.837 49 4 0 961 1009 123517119 123517071 7.620000e-08 69.4
38 TraesCS1D01G127400 chr7B 82.755 864 114 26 3333 4189 690044900 690044065 0.000000e+00 737.0
39 TraesCS1D01G127400 chr3A 92.938 439 31 0 1538 1976 746944720 746944282 1.290000e-179 640.0
40 TraesCS1D01G127400 chr3A 87.132 544 41 18 890 1433 746945393 746944879 1.320000e-164 590.0
41 TraesCS1D01G127400 chr3A 93.141 277 15 3 2692 2965 746944117 746943842 1.840000e-108 403.0
42 TraesCS1D01G127400 chr3A 88.000 175 18 3 224 396 200806307 200806134 2.000000e-48 204.0
43 TraesCS1D01G127400 chr3A 97.059 34 1 0 2608 2641 13522565 13522532 1.650000e-04 58.4
44 TraesCS1D01G127400 chr5A 89.080 174 16 3 234 405 17604078 17604250 3.330000e-51 213.0
45 TraesCS1D01G127400 chr2D 89.634 164 14 2 234 395 412716026 412716188 5.570000e-49 206.0
46 TraesCS1D01G127400 chr2D 89.091 165 15 3 234 397 76865263 76865101 7.200000e-48 202.0
47 TraesCS1D01G127400 chr2D 90.196 51 4 1 2591 2641 2827993 2827944 9.860000e-07 65.8
48 TraesCS1D01G127400 chr7D 89.506 162 15 2 234 394 453283662 453283502 2.000000e-48 204.0
49 TraesCS1D01G127400 chr7D 89.362 47 4 1 2595 2641 634386967 634386922 1.650000e-04 58.4
50 TraesCS1D01G127400 chr6D 89.506 162 15 2 235 395 394588599 394588759 2.000000e-48 204.0
51 TraesCS1D01G127400 chr6D 89.091 165 15 3 234 397 72143435 72143273 7.200000e-48 202.0
52 TraesCS1D01G127400 chr4D 89.157 166 15 2 231 394 240930272 240930436 2.000000e-48 204.0
53 TraesCS1D01G127400 chr2A 93.617 47 2 1 2595 2641 337606747 337606792 7.620000e-08 69.4
54 TraesCS1D01G127400 chr7A 94.872 39 1 1 2603 2641 19924023 19924060 4.590000e-05 60.2


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 TraesCS1D01G127400 chr1D 139978152 139982398 4246 False 3643.000000 6209 100.000000 1 4247 2 chr1D.!!$F1 4246
1 TraesCS1D01G127400 chr1A 150898431 150902571 4140 True 1149.500000 2185 91.172750 1 4247 4 chr1A.!!$R2 4246
2 TraesCS1D01G127400 chr1B 198642636 198645903 3267 True 599.040000 1140 89.866400 1 3322 5 chr1B.!!$R3 3321
3 TraesCS1D01G127400 chrUn 27216470 27217377 907 True 918.000000 918 85.065000 3333 4247 1 chrUn.!!$R1 914
4 TraesCS1D01G127400 chr5D 557520772 557521678 906 False 902.000000 902 84.740000 3333 4247 1 chr5D.!!$F1 914
5 TraesCS1D01G127400 chr3B 782666004 782666909 905 False 894.000000 894 84.698000 3333 4247 1 chr3B.!!$F1 914
6 TraesCS1D01G127400 chr3B 826711444 826712977 1533 False 557.666667 641 91.304333 886 2965 3 chr3B.!!$F3 2079
7 TraesCS1D01G127400 chr2B 8178859 8179767 908 False 876.000000 876 84.216000 3333 4247 1 chr2B.!!$F1 914
8 TraesCS1D01G127400 chr2B 408302163 408302986 823 False 797.000000 797 84.279000 3412 4247 1 chr2B.!!$F3 835
9 TraesCS1D01G127400 chr4B 613083520 613084428 908 False 809.000000 809 82.919000 3333 4247 1 chr4B.!!$F1 914
10 TraesCS1D01G127400 chr3D 609280084 609280979 895 False 747.000000 747 81.937000 3337 4244 1 chr3D.!!$F1 907
11 TraesCS1D01G127400 chr3D 612290291 612291777 1486 True 562.000000 645 90.688667 886 2965 3 chr3D.!!$R2 2079
12 TraesCS1D01G127400 chr7B 690044065 690044900 835 True 737.000000 737 82.755000 3333 4189 1 chr7B.!!$R1 856
13 TraesCS1D01G127400 chr3A 746943842 746945393 1551 True 544.333333 640 91.070333 890 2965 3 chr3A.!!$R3 2075

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
243 257 0.316204 CACGTACAAACTCCCTCCGT 59.684 55.0 0.0 0.0 0.00 4.69 F
1567 1773 0.178990 AGGAGTTTTTCGGCAAGGCT 60.179 50.0 0.0 0.0 0.00 4.58 F
2257 2551 0.111253 CAAGGCTGGTGTTCCTTCCT 59.889 55.0 0.0 0.0 40.50 3.36 F
2258 2552 0.402121 AAGGCTGGTGTTCCTTCCTC 59.598 55.0 0.0 0.0 38.21 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2437 0.106519 AAGGAAGGTGCACACTGCTT 60.107 50.0 20.43 17.49 45.31 3.91 R
3085 3856 0.595588 CATACCAAAACACGCAGGCA 59.404 50.0 0.00 0.00 0.00 4.75 R
3086 3857 0.596082 ACATACCAAAACACGCAGGC 59.404 50.0 0.00 0.00 0.00 4.85 R
4124 5005 1.464734 TTGAACAACTTCCGGCACAA 58.535 45.0 0.00 0.00 0.00 3.33 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
104 105 5.998363 GGCTAGTGGATTATGGTTAAGAAGG 59.002 44.000 0.00 0.00 0.00 3.46
105 106 6.409349 GGCTAGTGGATTATGGTTAAGAAGGT 60.409 42.308 0.00 0.00 0.00 3.50
107 108 6.636454 AGTGGATTATGGTTAAGAAGGTGA 57.364 37.500 0.00 0.00 0.00 4.02
109 110 8.331931 AGTGGATTATGGTTAAGAAGGTGATA 57.668 34.615 0.00 0.00 0.00 2.15
111 112 8.837389 GTGGATTATGGTTAAGAAGGTGATAAC 58.163 37.037 0.00 0.00 0.00 1.89
113 114 9.574516 GGATTATGGTTAAGAAGGTGATAACAT 57.425 33.333 0.00 0.00 32.47 2.71
146 148 2.524034 CGTGTGAGTCATAGCTGTCAG 58.476 52.381 0.00 0.00 0.00 3.51
231 245 0.687920 TCCCATCAAAGCCACGTACA 59.312 50.000 0.00 0.00 0.00 2.90
232 246 1.072489 TCCCATCAAAGCCACGTACAA 59.928 47.619 0.00 0.00 0.00 2.41
233 247 1.883275 CCCATCAAAGCCACGTACAAA 59.117 47.619 0.00 0.00 0.00 2.83
234 248 2.351350 CCCATCAAAGCCACGTACAAAC 60.351 50.000 0.00 0.00 0.00 2.93
235 249 2.552315 CCATCAAAGCCACGTACAAACT 59.448 45.455 0.00 0.00 0.00 2.66
236 250 3.364964 CCATCAAAGCCACGTACAAACTC 60.365 47.826 0.00 0.00 0.00 3.01
237 251 2.215196 TCAAAGCCACGTACAAACTCC 58.785 47.619 0.00 0.00 0.00 3.85
238 252 1.265905 CAAAGCCACGTACAAACTCCC 59.734 52.381 0.00 0.00 0.00 4.30
239 253 0.763035 AAGCCACGTACAAACTCCCT 59.237 50.000 0.00 0.00 0.00 4.20
240 254 0.320697 AGCCACGTACAAACTCCCTC 59.679 55.000 0.00 0.00 0.00 4.30
241 255 0.672711 GCCACGTACAAACTCCCTCC 60.673 60.000 0.00 0.00 0.00 4.30
242 256 0.389426 CCACGTACAAACTCCCTCCG 60.389 60.000 0.00 0.00 0.00 4.63
243 257 0.316204 CACGTACAAACTCCCTCCGT 59.684 55.000 0.00 0.00 0.00 4.69
244 258 1.043022 ACGTACAAACTCCCTCCGTT 58.957 50.000 0.00 0.00 0.00 4.44
245 259 1.000171 ACGTACAAACTCCCTCCGTTC 60.000 52.381 0.00 0.00 0.00 3.95
246 260 1.271656 CGTACAAACTCCCTCCGTTCT 59.728 52.381 0.00 0.00 0.00 3.01
247 261 2.288640 CGTACAAACTCCCTCCGTTCTT 60.289 50.000 0.00 0.00 0.00 2.52
248 262 3.057315 CGTACAAACTCCCTCCGTTCTTA 60.057 47.826 0.00 0.00 0.00 2.10
249 263 4.559300 CGTACAAACTCCCTCCGTTCTTAA 60.559 45.833 0.00 0.00 0.00 1.85
250 264 4.426736 ACAAACTCCCTCCGTTCTTAAA 57.573 40.909 0.00 0.00 0.00 1.52
251 265 4.981812 ACAAACTCCCTCCGTTCTTAAAT 58.018 39.130 0.00 0.00 0.00 1.40
252 266 6.117975 ACAAACTCCCTCCGTTCTTAAATA 57.882 37.500 0.00 0.00 0.00 1.40
253 267 6.718294 ACAAACTCCCTCCGTTCTTAAATAT 58.282 36.000 0.00 0.00 0.00 1.28
254 268 7.854337 ACAAACTCCCTCCGTTCTTAAATATA 58.146 34.615 0.00 0.00 0.00 0.86
255 269 8.323567 ACAAACTCCCTCCGTTCTTAAATATAA 58.676 33.333 0.00 0.00 0.00 0.98
256 270 8.827677 CAAACTCCCTCCGTTCTTAAATATAAG 58.172 37.037 0.00 0.00 39.97 1.73
257 271 7.672122 ACTCCCTCCGTTCTTAAATATAAGT 57.328 36.000 0.00 0.00 39.65 2.24
258 272 7.724287 ACTCCCTCCGTTCTTAAATATAAGTC 58.276 38.462 0.00 0.00 39.65 3.01
259 273 7.564292 ACTCCCTCCGTTCTTAAATATAAGTCT 59.436 37.037 0.00 0.00 39.65 3.24
260 274 8.315220 TCCCTCCGTTCTTAAATATAAGTCTT 57.685 34.615 0.00 0.00 39.65 3.01
261 275 8.765517 TCCCTCCGTTCTTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 39.65 2.52
262 276 8.827677 CCCTCCGTTCTTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 39.65 2.77
263 277 9.379791 CCTCCGTTCTTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 39.65 2.83
280 294 9.793259 AAGTCTTTGTAAAGATTTCACTATGGA 57.207 29.630 9.98 0.00 45.83 3.41
281 295 9.965902 AGTCTTTGTAAAGATTTCACTATGGAT 57.034 29.630 9.98 0.00 45.83 3.41
283 297 9.958180 TCTTTGTAAAGATTTCACTATGGATCA 57.042 29.630 3.05 0.00 39.95 2.92
284 298 9.994432 CTTTGTAAAGATTTCACTATGGATCAC 57.006 33.333 0.00 0.00 38.28 3.06
285 299 9.513906 TTTGTAAAGATTTCACTATGGATCACA 57.486 29.630 0.00 0.00 0.00 3.58
286 300 9.685276 TTGTAAAGATTTCACTATGGATCACAT 57.315 29.630 0.00 0.00 43.68 3.21
290 304 8.859236 AAGATTTCACTATGGATCACATATGG 57.141 34.615 7.80 0.00 41.07 2.74
291 305 8.211030 AGATTTCACTATGGATCACATATGGA 57.789 34.615 7.80 2.05 41.07 3.41
292 306 8.833734 AGATTTCACTATGGATCACATATGGAT 58.166 33.333 7.80 7.00 41.07 3.41
293 307 8.803397 ATTTCACTATGGATCACATATGGATG 57.197 34.615 7.80 0.00 41.07 3.51
294 308 5.737860 TCACTATGGATCACATATGGATGC 58.262 41.667 7.80 12.07 41.07 3.91
295 309 5.248934 TCACTATGGATCACATATGGATGCA 59.751 40.000 21.61 21.61 45.23 3.96
301 315 7.679732 TGGATCACATATGGATGCATATAGA 57.320 36.000 18.15 17.93 38.04 1.98
302 316 8.271398 TGGATCACATATGGATGCATATAGAT 57.729 34.615 22.88 22.88 38.04 1.98
303 317 8.154856 TGGATCACATATGGATGCATATAGATG 58.845 37.037 25.52 20.08 38.04 2.90
336 350 9.941664 AAGTATAGATTCATTCATTTTGCTTCG 57.058 29.630 0.00 0.00 0.00 3.79
337 351 9.113838 AGTATAGATTCATTCATTTTGCTTCGT 57.886 29.630 0.00 0.00 0.00 3.85
438 452 4.079970 CTCCATTCATCCATCCATCCTTG 58.920 47.826 0.00 0.00 0.00 3.61
480 529 2.085343 GCCCATCATAGGCCACCCAT 62.085 60.000 5.01 0.00 45.16 4.00
486 535 0.758734 CATAGGCCACCCATCGAGAA 59.241 55.000 5.01 0.00 0.00 2.87
490 539 1.144936 GCCACCCATCGAGAAGAGG 59.855 63.158 0.00 0.00 0.00 3.69
501 550 5.479306 CATCGAGAAGAGGAAGGTGTTTTA 58.521 41.667 0.00 0.00 31.12 1.52
529 578 0.666374 GCGGCATAATTACCACCACC 59.334 55.000 0.00 0.00 0.00 4.61
530 579 0.941542 CGGCATAATTACCACCACCG 59.058 55.000 0.00 0.00 0.00 4.94
531 580 0.666374 GGCATAATTACCACCACCGC 59.334 55.000 0.00 0.00 0.00 5.68
534 583 1.133915 CATAATTACCACCACCGCCCT 60.134 52.381 0.00 0.00 0.00 5.19
536 585 0.610785 AATTACCACCACCGCCCTTG 60.611 55.000 0.00 0.00 0.00 3.61
537 586 1.785353 ATTACCACCACCGCCCTTGT 61.785 55.000 0.00 0.00 0.00 3.16
538 587 2.684192 TTACCACCACCGCCCTTGTG 62.684 60.000 0.00 0.00 0.00 3.33
554 607 5.393896 GCCCTTGTGGTAGTAGTAGTAAGTG 60.394 48.000 0.00 0.00 36.04 3.16
569 622 1.750193 AAGTGGTAATCCATGTGCCG 58.250 50.000 0.00 0.00 46.20 5.69
580 633 3.659786 TCCATGTGCCGTGCTATATAAC 58.340 45.455 0.00 0.00 0.00 1.89
1200 1290 3.826157 GGTTGGGTTGACTGATTGATTGA 59.174 43.478 0.00 0.00 0.00 2.57
1203 1293 4.665451 TGGGTTGACTGATTGATTGATGT 58.335 39.130 0.00 0.00 0.00 3.06
1462 1557 1.463528 GCGCCGCTAGTAAACAACAAG 60.464 52.381 0.00 0.00 0.00 3.16
1475 1629 2.494059 ACAACAAGGAGACATCGGTTG 58.506 47.619 0.00 0.00 38.02 3.77
1477 1631 2.169832 ACAAGGAGACATCGGTTGTG 57.830 50.000 0.00 0.00 39.18 3.33
1478 1632 0.798776 CAAGGAGACATCGGTTGTGC 59.201 55.000 0.00 0.00 39.18 4.57
1479 1633 0.687354 AAGGAGACATCGGTTGTGCT 59.313 50.000 0.00 0.00 39.18 4.40
1480 1634 0.247736 AGGAGACATCGGTTGTGCTC 59.752 55.000 0.00 3.94 39.18 4.26
1503 1657 4.095782 CCAGTTTTCTTGTCCGTTTCTTGA 59.904 41.667 0.00 0.00 0.00 3.02
1504 1658 5.392595 CCAGTTTTCTTGTCCGTTTCTTGAA 60.393 40.000 0.00 0.00 0.00 2.69
1505 1659 6.090129 CAGTTTTCTTGTCCGTTTCTTGAAA 58.910 36.000 0.00 0.00 0.00 2.69
1512 1666 6.750039 TCTTGTCCGTTTCTTGAAATGAAAAC 59.250 34.615 14.71 10.66 40.94 2.43
1515 1669 6.309251 TGTCCGTTTCTTGAAATGAAAACAAC 59.691 34.615 14.71 5.84 40.94 3.32
1567 1773 0.178990 AGGAGTTTTTCGGCAAGGCT 60.179 50.000 0.00 0.00 0.00 4.58
1980 2186 1.749638 ACCTCTACGGTCAGCCTCG 60.750 63.158 0.00 0.00 44.93 4.63
1981 2187 2.482333 CCTCTACGGTCAGCCTCGG 61.482 68.421 0.00 0.00 0.00 4.63
2142 2404 1.756375 GCGCTAGCATGTCAGTTCCG 61.756 60.000 16.45 0.00 44.35 4.30
2171 2438 3.948719 GGGCGGTGACTGTGGGAA 61.949 66.667 0.00 0.00 0.00 3.97
2172 2439 2.358737 GGCGGTGACTGTGGGAAG 60.359 66.667 0.00 0.00 0.00 3.46
2173 2440 3.050275 GCGGTGACTGTGGGAAGC 61.050 66.667 0.00 0.00 0.00 3.86
2201 2468 4.142049 TGCACCTTCCTTTTGGTAGTTTTG 60.142 41.667 0.00 0.00 41.38 2.44
2257 2551 0.111253 CAAGGCTGGTGTTCCTTCCT 59.889 55.000 0.00 0.00 40.50 3.36
2258 2552 0.402121 AAGGCTGGTGTTCCTTCCTC 59.598 55.000 0.00 0.00 38.21 3.71
2442 2747 0.616371 CTAACACCGGGTTCCATCCA 59.384 55.000 6.32 0.00 40.96 3.41
2490 2795 2.427506 GCTTAATCTCCGCCCCATTAG 58.572 52.381 0.00 0.00 0.00 1.73
2526 2831 3.265791 CCATCTGCTTTACCTCACTGAC 58.734 50.000 0.00 0.00 0.00 3.51
2541 2895 5.067153 CCTCACTGACCTGATCTTAGTACTG 59.933 48.000 5.39 0.00 0.00 2.74
2551 2905 6.918569 CCTGATCTTAGTACTGATTAACACGG 59.081 42.308 5.39 0.00 0.00 4.94
2586 3147 7.803189 CACTCATTACGCAAAGACAACTTTAAT 59.197 33.333 0.00 0.00 43.41 1.40
2587 3148 8.349983 ACTCATTACGCAAAGACAACTTTAATT 58.650 29.630 0.00 0.00 43.41 1.40
2599 3160 9.730705 AAGACAACTTTAATTAAGTACTACCCC 57.269 33.333 0.00 0.00 46.34 4.95
2600 3161 8.324306 AGACAACTTTAATTAAGTACTACCCCC 58.676 37.037 0.00 0.00 46.34 5.40
2601 3162 8.223378 ACAACTTTAATTAAGTACTACCCCCT 57.777 34.615 0.00 0.00 46.34 4.79
2602 3163 8.324306 ACAACTTTAATTAAGTACTACCCCCTC 58.676 37.037 0.00 0.00 46.34 4.30
2603 3164 7.443302 ACTTTAATTAAGTACTACCCCCTCC 57.557 40.000 0.00 0.00 45.22 4.30
2604 3165 6.098838 ACTTTAATTAAGTACTACCCCCTCCG 59.901 42.308 0.00 0.00 45.22 4.63
2605 3166 3.695357 ATTAAGTACTACCCCCTCCGT 57.305 47.619 0.00 0.00 0.00 4.69
2606 3167 3.473113 TTAAGTACTACCCCCTCCGTT 57.527 47.619 0.00 0.00 0.00 4.44
2607 3168 4.601406 TTAAGTACTACCCCCTCCGTTA 57.399 45.455 0.00 0.00 0.00 3.18
2608 3169 3.473113 AAGTACTACCCCCTCCGTTAA 57.527 47.619 0.00 0.00 0.00 2.01
2609 3170 3.473113 AGTACTACCCCCTCCGTTAAA 57.527 47.619 0.00 0.00 0.00 1.52
2610 3171 3.369175 AGTACTACCCCCTCCGTTAAAG 58.631 50.000 0.00 0.00 0.00 1.85
2611 3172 1.576577 ACTACCCCCTCCGTTAAAGG 58.423 55.000 0.26 0.26 0.00 3.11
2612 3173 1.079323 ACTACCCCCTCCGTTAAAGGA 59.921 52.381 9.89 9.89 35.83 3.36
2613 3174 2.190538 CTACCCCCTCCGTTAAAGGAA 58.809 52.381 11.44 0.00 40.25 3.36
2614 3175 1.677490 ACCCCCTCCGTTAAAGGAAT 58.323 50.000 11.44 0.00 40.25 3.01
2615 3176 2.849537 ACCCCCTCCGTTAAAGGAATA 58.150 47.619 11.44 0.00 40.25 1.75
2616 3177 3.400419 ACCCCCTCCGTTAAAGGAATAT 58.600 45.455 11.44 0.00 40.25 1.28
2617 3178 4.569902 ACCCCCTCCGTTAAAGGAATATA 58.430 43.478 11.44 0.00 40.25 0.86
2618 3179 4.977090 ACCCCCTCCGTTAAAGGAATATAA 59.023 41.667 11.44 0.00 40.25 0.98
2619 3180 5.072736 ACCCCCTCCGTTAAAGGAATATAAG 59.927 44.000 11.44 0.00 40.25 1.73
2620 3181 5.308759 CCCCCTCCGTTAAAGGAATATAAGA 59.691 44.000 11.44 0.00 40.25 2.10
2621 3182 6.183361 CCCCCTCCGTTAAAGGAATATAAGAA 60.183 42.308 11.44 0.00 40.25 2.52
2622 3183 6.709397 CCCCTCCGTTAAAGGAATATAAGAAC 59.291 42.308 11.44 0.00 40.25 3.01
2623 3184 7.277396 CCCTCCGTTAAAGGAATATAAGAACA 58.723 38.462 11.44 0.00 40.25 3.18
2624 3185 7.937394 CCCTCCGTTAAAGGAATATAAGAACAT 59.063 37.037 11.44 0.00 40.25 2.71
2625 3186 9.338622 CCTCCGTTAAAGGAATATAAGAACATT 57.661 33.333 11.44 0.00 40.25 2.71
2647 3208 9.944376 ACATTTAGATCACTAAAGTAAAGCAGA 57.056 29.630 0.00 0.00 46.97 4.26
2651 3212 3.585862 TCACTAAAGTAAAGCAGAGCGG 58.414 45.455 0.00 0.00 0.00 5.52
2655 3216 4.691216 ACTAAAGTAAAGCAGAGCGGAAAG 59.309 41.667 0.00 0.00 0.00 2.62
2658 3219 3.067833 AGTAAAGCAGAGCGGAAAGAAC 58.932 45.455 0.00 0.00 0.00 3.01
2660 3221 1.517242 AAGCAGAGCGGAAAGAACAG 58.483 50.000 0.00 0.00 0.00 3.16
2670 3235 3.600388 CGGAAAGAACAGAGTATTGCCT 58.400 45.455 0.00 0.00 0.00 4.75
2684 3418 9.416794 CAGAGTATTGCCTAAGATAATGTGTAG 57.583 37.037 0.00 0.00 0.00 2.74
2685 3419 9.148879 AGAGTATTGCCTAAGATAATGTGTAGT 57.851 33.333 0.00 0.00 0.00 2.73
2704 3443 9.911138 TGTGTAGTAATGTTGTAATAACGAAGA 57.089 29.630 0.00 0.00 0.00 2.87
2712 3451 7.780008 TGTTGTAATAACGAAGATATGTGGG 57.220 36.000 0.00 0.00 0.00 4.61
2713 3452 6.259167 TGTTGTAATAACGAAGATATGTGGGC 59.741 38.462 0.00 0.00 0.00 5.36
2714 3453 5.919755 TGTAATAACGAAGATATGTGGGCA 58.080 37.500 0.00 0.00 0.00 5.36
2715 3454 6.350103 TGTAATAACGAAGATATGTGGGCAA 58.650 36.000 0.00 0.00 0.00 4.52
2716 3455 5.751243 AATAACGAAGATATGTGGGCAAC 57.249 39.130 0.00 0.00 0.00 4.17
2909 3659 1.455849 CAACACCTGGCTCAAGGGA 59.544 57.895 0.00 0.00 42.11 4.20
2992 3756 8.671384 AACTACTGTTATTAACACACACACAT 57.329 30.769 5.14 0.00 36.25 3.21
3084 3855 0.862490 TACAATTCCGTGTGCGTGTG 59.138 50.000 0.00 0.00 36.15 3.82
3085 3856 1.092921 ACAATTCCGTGTGCGTGTGT 61.093 50.000 0.00 0.00 36.15 3.72
3086 3857 0.657077 CAATTCCGTGTGCGTGTGTG 60.657 55.000 0.00 0.00 36.15 3.82
3087 3858 2.387125 AATTCCGTGTGCGTGTGTGC 62.387 55.000 0.00 0.00 36.15 4.57
3090 3861 4.297891 CGTGTGCGTGTGTGCCTG 62.298 66.667 0.00 0.00 0.00 4.85
3091 3862 4.612536 GTGTGCGTGTGTGCCTGC 62.613 66.667 0.00 0.00 0.00 4.85
3102 3873 0.748367 TGTGCCTGCGTGTTTTGGTA 60.748 50.000 0.00 0.00 0.00 3.25
3117 3891 8.609176 CGTGTTTTGGTATGTAATATGCTTAGT 58.391 33.333 0.00 0.00 0.00 2.24
3170 3946 1.535462 CTCCAATCTTTTTGACGCCGT 59.465 47.619 0.00 0.00 0.00 5.68
3171 3947 1.265635 TCCAATCTTTTTGACGCCGTG 59.734 47.619 0.00 0.00 0.00 4.94
3173 3949 2.043411 CAATCTTTTTGACGCCGTGTG 58.957 47.619 0.00 0.00 0.00 3.82
3174 3950 1.305201 ATCTTTTTGACGCCGTGTGT 58.695 45.000 0.00 0.00 0.00 3.72
3209 4005 3.947834 CTGAGTTGGGGACATTGTAATCC 59.052 47.826 0.00 0.00 42.32 3.01
3219 4015 5.124936 GGGACATTGTAATCCTTGGTTGTAC 59.875 44.000 0.00 0.00 35.15 2.90
3281 4082 4.930963 TGTGTTTGGCTGTAAATTGTGAG 58.069 39.130 0.00 0.00 0.00 3.51
3301 4102 1.990563 GATGTGTTCTCCGTGTTACCG 59.009 52.381 0.00 0.00 0.00 4.02
3326 4130 4.334481 TGAAACAAGTCCCTTCTTCGAAAC 59.666 41.667 0.00 0.00 0.00 2.78
3329 4133 4.461198 ACAAGTCCCTTCTTCGAAACAAT 58.539 39.130 0.00 0.00 0.00 2.71
3398 4204 9.519905 CAAAATATTTTTCAGAAATGCGAACAG 57.480 29.630 10.77 0.00 0.00 3.16
4124 5005 4.906065 AGACATGTCGCAATTTGCATAT 57.094 36.364 19.85 8.78 45.36 1.78
4206 5089 8.929487 AGTGGAAAATTTAGGGTAATTTCAACA 58.071 29.630 6.79 0.00 36.87 3.33
4213 5096 6.503589 TTAGGGTAATTTCAACAATGTCCG 57.496 37.500 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.171308 CCCTGTTGGAGAAGCACATG 58.829 55.000 0.00 0.00 35.39 3.21
43 44 3.611766 ACTATTTCGTCCCTGTTGGAG 57.388 47.619 0.00 0.00 46.38 3.86
104 105 6.590292 CACGGAAGGGATATGTATGTTATCAC 59.410 42.308 0.00 0.00 35.60 3.06
105 106 6.269077 ACACGGAAGGGATATGTATGTTATCA 59.731 38.462 0.00 0.00 38.45 2.15
107 108 6.269077 TCACACGGAAGGGATATGTATGTTAT 59.731 38.462 0.00 0.00 38.45 1.89
109 110 4.407621 TCACACGGAAGGGATATGTATGTT 59.592 41.667 0.00 0.00 38.45 2.71
111 112 4.039245 ACTCACACGGAAGGGATATGTATG 59.961 45.833 0.00 0.00 38.45 2.39
113 114 3.635373 GACTCACACGGAAGGGATATGTA 59.365 47.826 0.00 0.00 38.45 2.29
146 148 2.034687 AGGGCATGTGTCACCTGC 59.965 61.111 21.14 21.14 38.72 4.85
231 245 8.546322 ACTTATATTTAAGAACGGAGGGAGTTT 58.454 33.333 9.58 0.00 38.56 2.66
232 246 8.087303 ACTTATATTTAAGAACGGAGGGAGTT 57.913 34.615 9.58 0.00 38.56 3.01
233 247 7.564292 AGACTTATATTTAAGAACGGAGGGAGT 59.436 37.037 9.58 0.00 38.56 3.85
234 248 7.953752 AGACTTATATTTAAGAACGGAGGGAG 58.046 38.462 9.58 0.00 38.56 4.30
235 249 7.909485 AGACTTATATTTAAGAACGGAGGGA 57.091 36.000 9.58 0.00 38.56 4.20
236 250 8.827677 CAAAGACTTATATTTAAGAACGGAGGG 58.172 37.037 9.58 0.00 38.56 4.30
237 251 9.379791 ACAAAGACTTATATTTAAGAACGGAGG 57.620 33.333 9.58 0.00 38.56 4.30
254 268 9.793259 TCCATAGTGAAATCTTTACAAAGACTT 57.207 29.630 6.56 2.45 46.80 3.01
255 269 9.965902 ATCCATAGTGAAATCTTTACAAAGACT 57.034 29.630 6.56 3.09 46.80 3.24
258 272 9.994432 GTGATCCATAGTGAAATCTTTACAAAG 57.006 33.333 0.00 0.00 37.36 2.77
259 273 9.513906 TGTGATCCATAGTGAAATCTTTACAAA 57.486 29.630 0.00 0.00 0.00 2.83
260 274 9.685276 ATGTGATCCATAGTGAAATCTTTACAA 57.315 29.630 0.00 0.00 29.82 2.41
264 278 9.293404 CCATATGTGATCCATAGTGAAATCTTT 57.707 33.333 1.24 0.00 39.36 2.52
265 279 8.663167 TCCATATGTGATCCATAGTGAAATCTT 58.337 33.333 1.24 0.00 39.36 2.40
266 280 8.211030 TCCATATGTGATCCATAGTGAAATCT 57.789 34.615 1.24 0.00 39.36 2.40
267 281 8.890718 CATCCATATGTGATCCATAGTGAAATC 58.109 37.037 1.24 0.00 39.36 2.17
268 282 7.338703 GCATCCATATGTGATCCATAGTGAAAT 59.661 37.037 1.24 4.53 39.36 2.17
269 283 6.656270 GCATCCATATGTGATCCATAGTGAAA 59.344 38.462 1.24 3.17 39.36 2.69
270 284 6.175471 GCATCCATATGTGATCCATAGTGAA 58.825 40.000 1.24 0.00 39.36 3.18
271 285 5.248934 TGCATCCATATGTGATCCATAGTGA 59.751 40.000 1.24 8.11 39.36 3.41
272 286 5.493809 TGCATCCATATGTGATCCATAGTG 58.506 41.667 1.24 7.66 39.36 2.74
273 287 5.767277 TGCATCCATATGTGATCCATAGT 57.233 39.130 1.24 0.00 39.36 2.12
274 288 9.654663 CTATATGCATCCATATGTGATCCATAG 57.345 37.037 0.19 0.00 42.94 2.23
275 289 9.383578 TCTATATGCATCCATATGTGATCCATA 57.616 33.333 0.19 14.83 42.94 2.74
276 290 8.271398 TCTATATGCATCCATATGTGATCCAT 57.729 34.615 0.19 12.44 42.94 3.41
277 291 7.679732 TCTATATGCATCCATATGTGATCCA 57.320 36.000 0.19 1.53 42.94 3.41
278 292 8.549338 CATCTATATGCATCCATATGTGATCC 57.451 38.462 0.19 0.00 42.94 3.36
310 324 9.941664 CGAAGCAAAATGAATGAATCTATACTT 57.058 29.630 0.00 0.00 0.00 2.24
311 325 9.113838 ACGAAGCAAAATGAATGAATCTATACT 57.886 29.630 0.00 0.00 0.00 2.12
372 386 8.218488 GGTTGTACTTCCTCCATTCCTAAATAT 58.782 37.037 0.00 0.00 0.00 1.28
373 387 7.404980 AGGTTGTACTTCCTCCATTCCTAAATA 59.595 37.037 0.00 0.00 0.00 1.40
374 388 6.217693 AGGTTGTACTTCCTCCATTCCTAAAT 59.782 38.462 0.00 0.00 0.00 1.40
375 389 5.550403 AGGTTGTACTTCCTCCATTCCTAAA 59.450 40.000 0.00 0.00 0.00 1.85
376 390 5.098663 AGGTTGTACTTCCTCCATTCCTAA 58.901 41.667 0.00 0.00 0.00 2.69
377 391 4.695606 AGGTTGTACTTCCTCCATTCCTA 58.304 43.478 0.00 0.00 0.00 2.94
378 392 3.532102 AGGTTGTACTTCCTCCATTCCT 58.468 45.455 0.00 0.00 0.00 3.36
379 393 5.431179 TTAGGTTGTACTTCCTCCATTCC 57.569 43.478 11.53 0.00 35.51 3.01
380 394 6.235664 TGTTTAGGTTGTACTTCCTCCATTC 58.764 40.000 11.53 3.27 35.51 2.67
381 395 6.195600 TGTTTAGGTTGTACTTCCTCCATT 57.804 37.500 11.53 0.00 35.51 3.16
382 396 5.836024 TGTTTAGGTTGTACTTCCTCCAT 57.164 39.130 11.53 0.00 35.51 3.41
383 397 5.633655 TTGTTTAGGTTGTACTTCCTCCA 57.366 39.130 11.53 6.34 35.51 3.86
384 398 5.824097 TGTTTGTTTAGGTTGTACTTCCTCC 59.176 40.000 11.53 4.38 35.51 4.30
385 399 6.930667 TGTTTGTTTAGGTTGTACTTCCTC 57.069 37.500 11.53 1.53 35.51 3.71
386 400 7.706100 TTTGTTTGTTTAGGTTGTACTTCCT 57.294 32.000 12.52 12.52 37.80 3.36
422 436 2.158564 GGAAGCAAGGATGGATGGATGA 60.159 50.000 0.00 0.00 0.00 2.92
438 452 1.492599 AGCTATGGGAAGGAAGGAAGC 59.507 52.381 0.00 0.00 0.00 3.86
480 529 5.740290 ATAAAACACCTTCCTCTTCTCGA 57.260 39.130 0.00 0.00 0.00 4.04
486 535 6.208797 GCCTTGTTTATAAAACACCTTCCTCT 59.791 38.462 4.77 0.00 0.00 3.69
490 539 5.158494 CCGCCTTGTTTATAAAACACCTTC 58.842 41.667 4.77 0.00 0.00 3.46
501 550 4.890581 TGGTAATTATGCCGCCTTGTTTAT 59.109 37.500 0.00 0.00 33.27 1.40
529 578 2.097825 ACTACTACTACCACAAGGGCG 58.902 52.381 0.00 0.00 42.05 6.13
530 579 4.708909 ACTTACTACTACTACCACAAGGGC 59.291 45.833 0.00 0.00 42.05 5.19
531 580 5.126707 CCACTTACTACTACTACCACAAGGG 59.873 48.000 0.00 0.00 44.81 3.95
534 583 8.884124 ATTACCACTTACTACTACTACCACAA 57.116 34.615 0.00 0.00 0.00 3.33
536 585 7.557719 TGGATTACCACTTACTACTACTACCAC 59.442 40.741 0.00 0.00 41.77 4.16
537 586 7.642186 TGGATTACCACTTACTACTACTACCA 58.358 38.462 0.00 0.00 41.77 3.25
554 607 0.748005 AGCACGGCACATGGATTACC 60.748 55.000 0.00 0.00 0.00 2.85
1200 1290 4.986645 TCGGCTGCACGCACACAT 62.987 61.111 0.50 0.00 41.67 3.21
1242 1334 4.367023 CCCTTGTTCGCCGACGGA 62.367 66.667 20.50 0.00 40.63 4.69
1462 1557 0.741221 GGAGCACAACCGATGTCTCC 60.741 60.000 16.15 16.15 43.10 3.71
1475 1629 1.264288 CGGACAAGAAAACTGGAGCAC 59.736 52.381 0.00 0.00 0.00 4.40
1477 1631 1.594331 ACGGACAAGAAAACTGGAGC 58.406 50.000 0.00 0.00 0.00 4.70
1478 1632 3.877508 AGAAACGGACAAGAAAACTGGAG 59.122 43.478 0.00 0.00 0.00 3.86
1479 1633 3.881220 AGAAACGGACAAGAAAACTGGA 58.119 40.909 0.00 0.00 0.00 3.86
1480 1634 4.095782 TCAAGAAACGGACAAGAAAACTGG 59.904 41.667 0.00 0.00 0.00 4.00
1567 1773 0.249155 ACTCGCCGAACACGAAAAGA 60.249 50.000 0.00 0.00 39.39 2.52
1980 2186 1.075536 TCAAAGGAGGAAAAGGAGGCC 59.924 52.381 0.00 0.00 0.00 5.19
1981 2187 2.586648 TCAAAGGAGGAAAAGGAGGC 57.413 50.000 0.00 0.00 0.00 4.70
2163 2430 1.526686 TGCACACTGCTTCCCACAG 60.527 57.895 0.00 0.00 45.31 3.66
2164 2431 1.823470 GTGCACACTGCTTCCCACA 60.823 57.895 13.17 0.00 45.31 4.17
2165 2432 2.555547 GGTGCACACTGCTTCCCAC 61.556 63.158 20.43 0.00 45.31 4.61
2166 2433 2.203337 GGTGCACACTGCTTCCCA 60.203 61.111 20.43 0.00 45.31 4.37
2167 2434 1.518903 GAAGGTGCACACTGCTTCCC 61.519 60.000 20.43 0.00 45.31 3.97
2168 2435 1.518903 GGAAGGTGCACACTGCTTCC 61.519 60.000 26.57 26.57 45.31 3.46
2169 2436 0.536006 AGGAAGGTGCACACTGCTTC 60.536 55.000 20.43 19.84 45.31 3.86
2170 2437 0.106519 AAGGAAGGTGCACACTGCTT 60.107 50.000 20.43 17.49 45.31 3.91
2171 2438 0.106519 AAAGGAAGGTGCACACTGCT 60.107 50.000 20.43 12.28 45.31 4.24
2172 2439 0.746659 AAAAGGAAGGTGCACACTGC 59.253 50.000 20.43 11.72 45.29 4.40
2173 2440 1.067516 CCAAAAGGAAGGTGCACACTG 59.932 52.381 20.43 3.28 0.00 3.66
2184 2451 3.444388 ACGCACAAAACTACCAAAAGGAA 59.556 39.130 0.00 0.00 0.00 3.36
2223 2506 3.815407 CTTGTTGCCCTGGCCCTGT 62.815 63.158 5.57 0.00 41.09 4.00
2257 2551 1.000019 CCCCACTGTCCTACTCCGA 60.000 63.158 0.00 0.00 0.00 4.55
2258 2552 1.000019 TCCCCACTGTCCTACTCCG 60.000 63.158 0.00 0.00 0.00 4.63
2360 2654 2.574212 GCTATGCGTGCGTGTTGC 60.574 61.111 0.00 0.00 46.70 4.17
2361 2655 1.225827 CAGCTATGCGTGCGTGTTG 60.226 57.895 0.00 0.00 35.28 3.33
2362 2656 1.227999 AACAGCTATGCGTGCGTGTT 61.228 50.000 0.00 1.54 35.28 3.32
2490 2795 2.684881 CAGATGGCATTTGTGTCCCTAC 59.315 50.000 9.72 0.00 0.00 3.18
2526 2831 6.918569 CCGTGTTAATCAGTACTAAGATCAGG 59.081 42.308 0.00 0.00 0.00 3.86
2541 2895 2.276430 GCGTGCGCCGTGTTAATC 60.276 61.111 17.38 0.00 39.32 1.75
2551 2905 1.345176 GTAATGAGTGAGCGTGCGC 59.655 57.895 8.67 8.67 42.33 6.09
2586 3147 3.473113 AACGGAGGGGGTAGTACTTAA 57.527 47.619 0.00 0.00 0.00 1.85
2587 3148 4.601406 TTAACGGAGGGGGTAGTACTTA 57.399 45.455 0.00 0.00 0.00 2.24
2589 3150 3.369175 CTTTAACGGAGGGGGTAGTACT 58.631 50.000 0.00 0.00 0.00 2.73
2590 3151 2.432146 CCTTTAACGGAGGGGGTAGTAC 59.568 54.545 0.00 0.00 0.00 2.73
2596 3157 5.308759 TCTTATATTCCTTTAACGGAGGGGG 59.691 44.000 0.45 0.00 34.93 5.40
2597 3158 6.429521 TCTTATATTCCTTTAACGGAGGGG 57.570 41.667 0.45 0.00 34.93 4.79
2598 3159 7.277396 TGTTCTTATATTCCTTTAACGGAGGG 58.723 38.462 0.45 0.00 34.93 4.30
2599 3160 8.904099 ATGTTCTTATATTCCTTTAACGGAGG 57.096 34.615 0.45 0.00 33.89 4.30
2621 3182 9.944376 TCTGCTTTACTTTAGTGATCTAAATGT 57.056 29.630 0.00 5.17 42.75 2.71
2623 3184 9.103861 GCTCTGCTTTACTTTAGTGATCTAAAT 57.896 33.333 0.00 0.00 42.75 1.40
2624 3185 7.275779 CGCTCTGCTTTACTTTAGTGATCTAAA 59.724 37.037 0.00 0.00 41.87 1.85
2625 3186 6.752351 CGCTCTGCTTTACTTTAGTGATCTAA 59.248 38.462 0.00 0.00 34.76 2.10
2626 3187 6.266323 CGCTCTGCTTTACTTTAGTGATCTA 58.734 40.000 0.00 0.00 0.00 1.98
2627 3188 5.105752 CGCTCTGCTTTACTTTAGTGATCT 58.894 41.667 0.00 0.00 0.00 2.75
2628 3189 4.268884 CCGCTCTGCTTTACTTTAGTGATC 59.731 45.833 0.00 0.00 0.00 2.92
2629 3190 4.081642 TCCGCTCTGCTTTACTTTAGTGAT 60.082 41.667 0.00 0.00 0.00 3.06
2630 3191 3.257375 TCCGCTCTGCTTTACTTTAGTGA 59.743 43.478 0.00 0.00 0.00 3.41
2631 3192 3.585862 TCCGCTCTGCTTTACTTTAGTG 58.414 45.455 0.00 0.00 0.00 2.74
2632 3193 3.955650 TCCGCTCTGCTTTACTTTAGT 57.044 42.857 0.00 0.00 0.00 2.24
2633 3194 4.929808 TCTTTCCGCTCTGCTTTACTTTAG 59.070 41.667 0.00 0.00 0.00 1.85
2634 3195 4.890088 TCTTTCCGCTCTGCTTTACTTTA 58.110 39.130 0.00 0.00 0.00 1.85
2635 3196 3.740115 TCTTTCCGCTCTGCTTTACTTT 58.260 40.909 0.00 0.00 0.00 2.66
2636 3197 3.402628 TCTTTCCGCTCTGCTTTACTT 57.597 42.857 0.00 0.00 0.00 2.24
2637 3198 3.067833 GTTCTTTCCGCTCTGCTTTACT 58.932 45.455 0.00 0.00 0.00 2.24
2638 3199 2.806244 TGTTCTTTCCGCTCTGCTTTAC 59.194 45.455 0.00 0.00 0.00 2.01
2639 3200 3.067106 CTGTTCTTTCCGCTCTGCTTTA 58.933 45.455 0.00 0.00 0.00 1.85
2640 3201 1.876156 CTGTTCTTTCCGCTCTGCTTT 59.124 47.619 0.00 0.00 0.00 3.51
2641 3202 1.070758 TCTGTTCTTTCCGCTCTGCTT 59.929 47.619 0.00 0.00 0.00 3.91
2642 3203 0.681733 TCTGTTCTTTCCGCTCTGCT 59.318 50.000 0.00 0.00 0.00 4.24
2643 3204 1.074752 CTCTGTTCTTTCCGCTCTGC 58.925 55.000 0.00 0.00 0.00 4.26
2644 3205 2.447244 ACTCTGTTCTTTCCGCTCTG 57.553 50.000 0.00 0.00 0.00 3.35
2645 3206 4.499183 CAATACTCTGTTCTTTCCGCTCT 58.501 43.478 0.00 0.00 0.00 4.09
2646 3207 3.062774 GCAATACTCTGTTCTTTCCGCTC 59.937 47.826 0.00 0.00 0.00 5.03
2647 3208 3.003480 GCAATACTCTGTTCTTTCCGCT 58.997 45.455 0.00 0.00 0.00 5.52
2648 3209 2.096013 GGCAATACTCTGTTCTTTCCGC 59.904 50.000 0.00 0.00 0.00 5.54
2651 3212 9.601217 TTATCTTAGGCAATACTCTGTTCTTTC 57.399 33.333 0.00 0.00 0.00 2.62
2655 3216 8.768955 CACATTATCTTAGGCAATACTCTGTTC 58.231 37.037 0.00 0.00 0.00 3.18
2658 3219 9.416794 CTACACATTATCTTAGGCAATACTCTG 57.583 37.037 0.00 0.00 0.00 3.35
2686 3420 8.836413 CCCACATATCTTCGTTATTACAACATT 58.164 33.333 0.00 0.00 0.00 2.71
2687 3421 7.041372 GCCCACATATCTTCGTTATTACAACAT 60.041 37.037 0.00 0.00 0.00 2.71
2688 3422 6.259167 GCCCACATATCTTCGTTATTACAACA 59.741 38.462 0.00 0.00 0.00 3.33
2689 3423 6.259167 TGCCCACATATCTTCGTTATTACAAC 59.741 38.462 0.00 0.00 0.00 3.32
2690 3424 6.350103 TGCCCACATATCTTCGTTATTACAA 58.650 36.000 0.00 0.00 0.00 2.41
2702 3441 2.579873 GCATCAGTTGCCCACATATCT 58.420 47.619 0.00 0.00 46.15 1.98
2713 3452 3.005554 CTCTTGTACCCTGCATCAGTTG 58.994 50.000 0.00 0.00 0.00 3.16
2714 3453 2.026822 CCTCTTGTACCCTGCATCAGTT 60.027 50.000 0.00 0.00 0.00 3.16
2715 3454 1.556911 CCTCTTGTACCCTGCATCAGT 59.443 52.381 0.00 0.00 0.00 3.41
2716 3455 1.134280 CCCTCTTGTACCCTGCATCAG 60.134 57.143 0.00 0.00 0.00 2.90
2992 3756 6.611236 TGTAGTTTAGTCATGGAGGATCATCA 59.389 38.462 9.94 0.00 36.25 3.07
3084 3855 0.596082 ATACCAAAACACGCAGGCAC 59.404 50.000 0.00 0.00 0.00 5.01
3085 3856 0.595588 CATACCAAAACACGCAGGCA 59.404 50.000 0.00 0.00 0.00 4.75
3086 3857 0.596082 ACATACCAAAACACGCAGGC 59.404 50.000 0.00 0.00 0.00 4.85
3087 3858 4.695217 ATTACATACCAAAACACGCAGG 57.305 40.909 0.00 0.00 0.00 4.85
3088 3859 5.681105 GCATATTACATACCAAAACACGCAG 59.319 40.000 0.00 0.00 0.00 5.18
3089 3860 5.355630 AGCATATTACATACCAAAACACGCA 59.644 36.000 0.00 0.00 0.00 5.24
3090 3861 5.816919 AGCATATTACATACCAAAACACGC 58.183 37.500 0.00 0.00 0.00 5.34
3091 3862 8.609176 ACTAAGCATATTACATACCAAAACACG 58.391 33.333 0.00 0.00 0.00 4.49
3117 3891 3.427909 CGTGACACGGCCTATGTAACTTA 60.428 47.826 20.26 0.40 38.08 2.24
3170 3946 1.693606 TCAGATCAAGACAGGCACACA 59.306 47.619 0.00 0.00 0.00 3.72
3171 3947 2.289320 ACTCAGATCAAGACAGGCACAC 60.289 50.000 0.00 0.00 0.00 3.82
3173 3949 2.740981 CAACTCAGATCAAGACAGGCAC 59.259 50.000 0.00 0.00 0.00 5.01
3174 3950 2.289882 CCAACTCAGATCAAGACAGGCA 60.290 50.000 0.00 0.00 0.00 4.75
3209 4005 5.446143 TTACTTGCCAATGTACAACCAAG 57.554 39.130 18.50 18.50 36.62 3.61
3219 4015 6.377327 ACCTAATCGATTTACTTGCCAATG 57.623 37.500 17.19 0.00 0.00 2.82
3249 4045 2.667481 CAGCCAAACACAACAACAACAG 59.333 45.455 0.00 0.00 0.00 3.16
3251 4047 2.682836 ACAGCCAAACACAACAACAAC 58.317 42.857 0.00 0.00 0.00 3.32
3262 4058 5.630680 CACATCTCACAATTTACAGCCAAAC 59.369 40.000 0.00 0.00 0.00 2.93
3263 4059 5.301551 ACACATCTCACAATTTACAGCCAAA 59.698 36.000 0.00 0.00 0.00 3.28
3281 4082 1.990563 CGGTAACACGGAGAACACATC 59.009 52.381 0.00 0.00 0.00 3.06
3326 4130 9.619316 TGTTCTCCGAAAATGTTTGTTATATTG 57.381 29.630 0.00 0.00 0.00 1.90
3329 4133 9.004717 TCATGTTCTCCGAAAATGTTTGTTATA 57.995 29.630 6.64 0.00 0.00 0.98
3398 4204 9.965824 TTAGAACACCTTTTTGATTTCATCTTC 57.034 29.630 0.00 0.00 0.00 2.87
3525 4339 2.686816 CCCAACTAAACGGCGGCAG 61.687 63.158 13.24 7.51 0.00 4.85
3850 4721 3.253432 GCTAGGTGTGAAGGAAAAAGGTG 59.747 47.826 0.00 0.00 0.00 4.00
4099 4980 2.159531 GCAAATTGCGACATGTCTAGCA 60.160 45.455 22.95 21.53 37.89 3.49
4124 5005 1.464734 TTGAACAACTTCCGGCACAA 58.535 45.000 0.00 0.00 0.00 3.33
4206 5089 5.067936 TGAACATGGTGTTTTTACGGACATT 59.932 36.000 0.00 0.00 41.28 2.71
4213 5096 4.922719 TCCGTTGAACATGGTGTTTTTAC 58.077 39.130 0.00 0.00 41.28 2.01


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

AutoCloner maintained by Alex Coulton.