Multiple sequence alignment - TraesCS5D01G427400

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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 TraesCS5D01G427400 chr5D 100.000 2426 0 0 1 2426 485601696 485604121 0.000000e+00 4481.0
1 TraesCS5D01G427400 chr5D 93.583 748 30 5 691 1435 485765893 485766625 0.000000e+00 1099.0
2 TraesCS5D01G427400 chr5D 90.775 748 59 7 691 1435 485917935 485918675 0.000000e+00 990.0
3 TraesCS5D01G427400 chr5D 84.241 863 82 24 691 1526 485737977 485738812 0.000000e+00 791.0
4 TraesCS5D01G427400 chr5D 83.097 775 87 24 695 1435 485354341 485355105 0.000000e+00 665.0
5 TraesCS5D01G427400 chr5D 82.763 760 85 26 691 1431 485350517 485351249 9.460000e-179 636.0
6 TraesCS5D01G427400 chr5D 86.491 570 60 6 880 1435 485274666 485275232 5.730000e-171 610.0
7 TraesCS5D01G427400 chr5D 80.000 780 78 40 691 1435 485375152 485375888 2.780000e-139 505.0
8 TraesCS5D01G427400 chr5D 92.553 188 7 4 1433 1619 485766673 485766854 1.850000e-66 263.0
9 TraesCS5D01G427400 chr5D 86.900 229 30 0 1206 1434 485611046 485611274 8.610000e-65 257.0
10 TraesCS5D01G427400 chr5D 87.838 222 23 3 342 560 520281563 520281343 8.610000e-65 257.0
11 TraesCS5D01G427400 chr5D 92.818 181 5 5 7 180 485765688 485765867 3.100000e-64 255.0
12 TraesCS5D01G427400 chr5D 91.005 189 8 6 1433 1619 485918727 485918908 1.860000e-61 246.0
13 TraesCS5D01G427400 chr5D 92.308 130 7 3 564 692 260675837 260675964 5.330000e-42 182.0
14 TraesCS5D01G427400 chr5D 92.800 125 9 0 2301 2425 485918925 485919049 5.330000e-42 182.0
15 TraesCS5D01G427400 chr5D 90.769 130 8 3 2301 2426 485766871 485767000 1.150000e-38 171.0
16 TraesCS5D01G427400 chr5B 91.270 756 53 6 691 1433 596972264 596973019 0.000000e+00 1018.0
17 TraesCS5D01G427400 chr5B 83.134 753 89 17 709 1428 596908611 596909358 0.000000e+00 652.0
18 TraesCS5D01G427400 chr5B 83.952 673 87 14 781 1435 596918313 596918982 2.050000e-175 625.0
19 TraesCS5D01G427400 chr5B 82.194 775 88 25 695 1435 596933244 596934002 2.650000e-174 621.0
20 TraesCS5D01G427400 chr5B 88.339 283 24 2 1162 1435 596914282 596914564 5.000000e-87 331.0
21 TraesCS5D01G427400 chr5B 95.238 126 5 1 2301 2426 596979425 596979549 5.290000e-47 198.0
22 TraesCS5D01G427400 chr5B 89.922 129 12 1 564 692 455258046 455258173 5.370000e-37 165.0
23 TraesCS5D01G427400 chr5B 91.270 126 4 5 1433 1557 596973070 596973189 5.370000e-37 165.0
24 TraesCS5D01G427400 chr5B 89.922 129 8 2 567 694 55034735 55034611 6.940000e-36 161.0
25 TraesCS5D01G427400 chr5B 79.487 117 12 11 1413 1524 596909388 596909497 3.350000e-09 73.1
26 TraesCS5D01G427400 chr1D 92.846 671 47 1 1620 2290 375352690 375353359 0.000000e+00 972.0
27 TraesCS5D01G427400 chr1D 91.641 658 51 3 1630 2286 469610148 469610802 0.000000e+00 907.0
28 TraesCS5D01G427400 chr1D 91.058 671 59 1 1620 2290 389330474 389331143 0.000000e+00 905.0
29 TraesCS5D01G427400 chr5A 86.784 908 59 20 691 1557 606558166 606559053 0.000000e+00 955.0
30 TraesCS5D01G427400 chr5A 83.268 771 90 17 691 1428 606541870 606542634 0.000000e+00 673.0
31 TraesCS5D01G427400 chr5A 94.521 219 10 1 691 907 606684239 606684457 1.070000e-88 337.0
32 TraesCS5D01G427400 chr5A 87.879 198 11 8 1 197 606684041 606684226 1.130000e-53 220.0
33 TraesCS5D01G427400 chr5A 88.950 181 11 6 1 180 606557968 606558140 5.250000e-52 215.0
34 TraesCS5D01G427400 chr5A 93.651 126 8 0 2301 2426 606559100 606559225 3.180000e-44 189.0
35 TraesCS5D01G427400 chr5A 82.418 91 6 8 1436 1524 606532178 606532260 1.200000e-08 71.3
36 TraesCS5D01G427400 chr7A 92.101 671 52 1 1620 2290 6799710 6799041 0.000000e+00 944.0
37 TraesCS5D01G427400 chr6D 91.791 670 52 3 1620 2287 68328727 68329395 0.000000e+00 929.0
38 TraesCS5D01G427400 chr6D 91.085 673 56 4 1620 2290 382344193 382343523 0.000000e+00 907.0
39 TraesCS5D01G427400 chr6D 79.733 375 60 12 201 565 60459455 60459087 8.610000e-65 257.0
40 TraesCS5D01G427400 chr7D 91.554 663 56 0 1620 2282 80326438 80327100 0.000000e+00 915.0
41 TraesCS5D01G427400 chr7D 90.963 675 56 5 1621 2290 120303935 120304609 0.000000e+00 904.0
42 TraesCS5D01G427400 chr4D 91.058 671 55 3 1620 2290 99207613 99206948 0.000000e+00 902.0
43 TraesCS5D01G427400 chr4D 81.299 385 44 21 206 569 285748479 285748102 1.100000e-73 287.0
44 TraesCS5D01G427400 chr2D 80.688 378 53 17 207 569 75398960 75399332 2.380000e-70 276.0
45 TraesCS5D01G427400 chr3A 79.508 366 65 9 203 565 36771256 36771614 4.000000e-63 252.0
46 TraesCS5D01G427400 chr3A 89.216 204 19 3 365 565 171346548 171346345 4.000000e-63 252.0
47 TraesCS5D01G427400 chr6B 84.921 252 24 9 440 687 156478725 156478484 2.410000e-60 243.0
48 TraesCS5D01G427400 chr6B 89.552 134 14 0 564 697 671139744 671139877 1.150000e-38 171.0
49 TraesCS5D01G427400 chr3B 78.497 386 52 20 207 570 454674514 454674890 8.730000e-55 224.0
50 TraesCS5D01G427400 chr2A 84.889 225 29 5 342 565 699975695 699975915 3.140000e-54 222.0
51 TraesCS5D01G427400 chr2B 91.538 130 9 2 564 693 749824993 749825120 6.890000e-41 178.0
52 TraesCS5D01G427400 chr7B 90.551 127 9 3 568 694 480328150 480328027 5.370000e-37 165.0
53 TraesCS5D01G427400 chr3D 90.476 126 11 1 567 692 72042235 72042111 5.370000e-37 165.0
54 TraesCS5D01G427400 chr6A 89.922 129 9 4 567 693 597747920 597747794 1.930000e-36 163.0


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 TraesCS5D01G427400 chr5D 485601696 485604121 2425 False 4481.000000 4481 100.000000 1 2426 1 chr5D.!!$F4 2425
1 TraesCS5D01G427400 chr5D 485737977 485738812 835 False 791.000000 791 84.241000 691 1526 1 chr5D.!!$F6 835
2 TraesCS5D01G427400 chr5D 485350517 485355105 4588 False 650.500000 665 82.930000 691 1435 2 chr5D.!!$F7 744
3 TraesCS5D01G427400 chr5D 485274666 485275232 566 False 610.000000 610 86.491000 880 1435 1 chr5D.!!$F2 555
4 TraesCS5D01G427400 chr5D 485375152 485375888 736 False 505.000000 505 80.000000 691 1435 1 chr5D.!!$F3 744
5 TraesCS5D01G427400 chr5D 485917935 485919049 1114 False 472.666667 990 91.526667 691 2425 3 chr5D.!!$F9 1734
6 TraesCS5D01G427400 chr5D 485765688 485767000 1312 False 447.000000 1099 92.430750 7 2426 4 chr5D.!!$F8 2419
7 TraesCS5D01G427400 chr5B 596933244 596934002 758 False 621.000000 621 82.194000 695 1435 1 chr5B.!!$F2 740
8 TraesCS5D01G427400 chr5B 596972264 596973189 925 False 591.500000 1018 91.270000 691 1557 2 chr5B.!!$F6 866
9 TraesCS5D01G427400 chr5B 596914282 596918982 4700 False 478.000000 625 86.145500 781 1435 2 chr5B.!!$F5 654
10 TraesCS5D01G427400 chr5B 596908611 596909497 886 False 362.550000 652 81.310500 709 1524 2 chr5B.!!$F4 815
11 TraesCS5D01G427400 chr1D 375352690 375353359 669 False 972.000000 972 92.846000 1620 2290 1 chr1D.!!$F1 670
12 TraesCS5D01G427400 chr1D 469610148 469610802 654 False 907.000000 907 91.641000 1630 2286 1 chr1D.!!$F3 656
13 TraesCS5D01G427400 chr1D 389330474 389331143 669 False 905.000000 905 91.058000 1620 2290 1 chr1D.!!$F2 670
14 TraesCS5D01G427400 chr5A 606541870 606542634 764 False 673.000000 673 83.268000 691 1428 1 chr5A.!!$F2 737
15 TraesCS5D01G427400 chr5A 606557968 606559225 1257 False 453.000000 955 89.795000 1 2426 3 chr5A.!!$F3 2425
16 TraesCS5D01G427400 chr7A 6799041 6799710 669 True 944.000000 944 92.101000 1620 2290 1 chr7A.!!$R1 670
17 TraesCS5D01G427400 chr6D 68328727 68329395 668 False 929.000000 929 91.791000 1620 2287 1 chr6D.!!$F1 667
18 TraesCS5D01G427400 chr6D 382343523 382344193 670 True 907.000000 907 91.085000 1620 2290 1 chr6D.!!$R2 670
19 TraesCS5D01G427400 chr7D 80326438 80327100 662 False 915.000000 915 91.554000 1620 2282 1 chr7D.!!$F1 662
20 TraesCS5D01G427400 chr7D 120303935 120304609 674 False 904.000000 904 90.963000 1621 2290 1 chr7D.!!$F2 669
21 TraesCS5D01G427400 chr4D 99206948 99207613 665 True 902.000000 902 91.058000 1620 2290 1 chr4D.!!$R1 670

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
679 688 0.104304 CCGCCCTTCACGTATAGCTT 59.896 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 9354 0.098376 CAGCGGCTTCTTGAAGATGC 59.902 55.0 20.86 20.86 42.61 3.91 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
152 161 6.402983 GCATTTGAAGATAGACCAAGACAGTG 60.403 42.308 0.00 0.00 0.00 3.66
180 189 0.313043 TTCCCGAGAACGTGTGACTC 59.687 55.000 0.00 0.00 37.88 3.36
181 190 0.820482 TCCCGAGAACGTGTGACTCA 60.820 55.000 0.00 0.00 37.88 3.41
183 192 0.311165 CCGAGAACGTGTGACTCACT 59.689 55.000 10.54 0.00 44.16 3.41
184 193 1.534163 CCGAGAACGTGTGACTCACTA 59.466 52.381 10.54 0.00 44.16 2.74
197 206 0.459237 CTCACTAAGCCAGACAGCCG 60.459 60.000 0.00 0.00 0.00 5.52
201 210 0.175760 CTAAGCCAGACAGCCGCTTA 59.824 55.000 0.00 0.00 42.60 3.09
203 212 0.250727 AAGCCAGACAGCCGCTTAAA 60.251 50.000 0.00 0.00 40.94 1.52
208 217 2.350522 CAGACAGCCGCTTAAATGACT 58.649 47.619 0.00 0.00 0.00 3.41
209 218 3.521560 CAGACAGCCGCTTAAATGACTA 58.478 45.455 0.00 0.00 0.00 2.59
210 219 3.553511 CAGACAGCCGCTTAAATGACTAG 59.446 47.826 0.00 0.00 0.00 2.57
211 220 3.195825 AGACAGCCGCTTAAATGACTAGT 59.804 43.478 0.00 0.00 0.00 2.57
213 222 2.609459 CAGCCGCTTAAATGACTAGTGG 59.391 50.000 0.00 0.00 41.43 4.00
214 223 2.236395 AGCCGCTTAAATGACTAGTGGT 59.764 45.455 0.00 0.00 40.77 4.16
215 224 3.007635 GCCGCTTAAATGACTAGTGGTT 58.992 45.455 0.00 0.00 40.77 3.67
216 225 3.181510 GCCGCTTAAATGACTAGTGGTTG 60.182 47.826 0.00 0.00 40.77 3.77
218 227 3.374058 CGCTTAAATGACTAGTGGTTGGG 59.626 47.826 0.00 0.00 0.00 4.12
219 228 3.694566 GCTTAAATGACTAGTGGTTGGGG 59.305 47.826 0.00 0.00 0.00 4.96
220 229 2.215942 AAATGACTAGTGGTTGGGGC 57.784 50.000 0.00 0.00 0.00 5.80
223 232 1.079336 GACTAGTGGTTGGGGCGTC 60.079 63.158 0.00 0.00 0.00 5.19
225 234 1.375523 CTAGTGGTTGGGGCGTCAC 60.376 63.158 0.00 0.00 0.00 3.67
227 236 4.265056 GTGGTTGGGGCGTCACCT 62.265 66.667 0.00 0.00 39.10 4.00
250 259 2.358737 CGCCGCTTGAGGGAAGTT 60.359 61.111 0.00 0.00 33.73 2.66
251 260 2.680913 CGCCGCTTGAGGGAAGTTG 61.681 63.158 0.00 0.00 33.73 3.16
252 261 1.600916 GCCGCTTGAGGGAAGTTGT 60.601 57.895 0.00 0.00 33.73 3.32
253 262 1.856265 GCCGCTTGAGGGAAGTTGTG 61.856 60.000 0.00 0.00 33.73 3.33
255 264 1.165907 CGCTTGAGGGAAGTTGTGCA 61.166 55.000 0.00 0.00 33.73 4.57
256 265 1.251251 GCTTGAGGGAAGTTGTGCAT 58.749 50.000 0.00 0.00 33.73 3.96
257 266 2.436417 GCTTGAGGGAAGTTGTGCATA 58.564 47.619 0.00 0.00 33.73 3.14
258 267 3.019564 GCTTGAGGGAAGTTGTGCATAT 58.980 45.455 0.00 0.00 33.73 1.78
259 268 3.181493 GCTTGAGGGAAGTTGTGCATATG 60.181 47.826 0.00 0.00 33.73 1.78
260 269 3.719268 TGAGGGAAGTTGTGCATATGT 57.281 42.857 4.29 0.00 0.00 2.29
261 270 4.032960 TGAGGGAAGTTGTGCATATGTT 57.967 40.909 4.29 0.00 0.00 2.71
262 271 4.406456 TGAGGGAAGTTGTGCATATGTTT 58.594 39.130 4.29 0.00 0.00 2.83
265 274 6.663093 TGAGGGAAGTTGTGCATATGTTTTAT 59.337 34.615 4.29 0.00 0.00 1.40
266 275 7.178274 TGAGGGAAGTTGTGCATATGTTTTATT 59.822 33.333 4.29 0.00 0.00 1.40
267 276 7.906327 AGGGAAGTTGTGCATATGTTTTATTT 58.094 30.769 4.29 0.00 0.00 1.40
268 277 8.374743 AGGGAAGTTGTGCATATGTTTTATTTT 58.625 29.630 4.29 0.00 0.00 1.82
292 301 6.681729 TTAAAACACATAGAGTCCTCACCT 57.318 37.500 0.00 0.00 0.00 4.00
293 302 5.568620 AAAACACATAGAGTCCTCACCTT 57.431 39.130 0.00 0.00 0.00 3.50
295 304 4.810191 ACACATAGAGTCCTCACCTTTC 57.190 45.455 0.00 0.00 0.00 2.62
296 305 4.160329 ACACATAGAGTCCTCACCTTTCA 58.840 43.478 0.00 0.00 0.00 2.69
297 306 4.780021 ACACATAGAGTCCTCACCTTTCAT 59.220 41.667 0.00 0.00 0.00 2.57
299 308 5.128499 CACATAGAGTCCTCACCTTTCATCT 59.872 44.000 0.00 0.00 0.00 2.90
300 309 6.322456 CACATAGAGTCCTCACCTTTCATCTA 59.678 42.308 0.00 0.00 0.00 1.98
301 310 6.897966 ACATAGAGTCCTCACCTTTCATCTAA 59.102 38.462 0.00 0.00 0.00 2.10
303 312 6.688073 AGAGTCCTCACCTTTCATCTAAAA 57.312 37.500 0.00 0.00 0.00 1.52
304 313 6.706295 AGAGTCCTCACCTTTCATCTAAAAG 58.294 40.000 0.00 0.00 36.26 2.27
305 314 6.498651 AGAGTCCTCACCTTTCATCTAAAAGA 59.501 38.462 0.00 0.00 38.30 2.52
306 315 7.016661 AGAGTCCTCACCTTTCATCTAAAAGAA 59.983 37.037 0.00 0.00 38.30 2.52
308 317 7.998964 AGTCCTCACCTTTCATCTAAAAGAAAA 59.001 33.333 0.00 0.00 38.30 2.29
309 318 8.797438 GTCCTCACCTTTCATCTAAAAGAAAAT 58.203 33.333 0.00 0.00 38.30 1.82
375 384 8.451908 AATAATTACCACTTCAGCCTATCAAC 57.548 34.615 0.00 0.00 0.00 3.18
376 385 4.901197 TTACCACTTCAGCCTATCAACA 57.099 40.909 0.00 0.00 0.00 3.33
377 386 3.788227 ACCACTTCAGCCTATCAACAA 57.212 42.857 0.00 0.00 0.00 2.83
378 387 3.679389 ACCACTTCAGCCTATCAACAAG 58.321 45.455 0.00 0.00 0.00 3.16
379 388 3.073062 ACCACTTCAGCCTATCAACAAGT 59.927 43.478 0.00 0.00 0.00 3.16
381 390 3.077359 ACTTCAGCCTATCAACAAGTGC 58.923 45.455 0.00 0.00 0.00 4.40
382 391 2.113860 TCAGCCTATCAACAAGTGCC 57.886 50.000 0.00 0.00 0.00 5.01
383 392 1.350684 TCAGCCTATCAACAAGTGCCA 59.649 47.619 0.00 0.00 0.00 4.92
384 393 1.470098 CAGCCTATCAACAAGTGCCAC 59.530 52.381 0.00 0.00 0.00 5.01
389 398 4.379499 GCCTATCAACAAGTGCCACTTTAC 60.379 45.833 7.51 0.00 36.03 2.01
393 402 4.203226 TCAACAAGTGCCACTTTACATGA 58.797 39.130 7.51 7.23 36.03 3.07
394 403 4.036262 TCAACAAGTGCCACTTTACATGAC 59.964 41.667 7.51 0.00 36.03 3.06
395 404 2.884639 ACAAGTGCCACTTTACATGACC 59.115 45.455 7.51 0.00 36.03 4.02
396 405 2.200373 AGTGCCACTTTACATGACCC 57.800 50.000 0.00 0.00 0.00 4.46
397 406 1.705186 AGTGCCACTTTACATGACCCT 59.295 47.619 0.00 0.00 0.00 4.34
399 408 2.890945 GTGCCACTTTACATGACCCTTT 59.109 45.455 0.00 0.00 0.00 3.11
400 409 4.076394 GTGCCACTTTACATGACCCTTTA 58.924 43.478 0.00 0.00 0.00 1.85
401 410 4.705023 GTGCCACTTTACATGACCCTTTAT 59.295 41.667 0.00 0.00 0.00 1.40
402 411 5.185056 GTGCCACTTTACATGACCCTTTATT 59.815 40.000 0.00 0.00 0.00 1.40
403 412 5.777732 TGCCACTTTACATGACCCTTTATTT 59.222 36.000 0.00 0.00 0.00 1.40
405 414 7.451877 TGCCACTTTACATGACCCTTTATTTAA 59.548 33.333 0.00 0.00 0.00 1.52
406 415 8.308207 GCCACTTTACATGACCCTTTATTTAAA 58.692 33.333 0.00 0.00 0.00 1.52
425 434 3.345508 AAAAATACCCGAGGTCCTCAC 57.654 47.619 19.15 0.00 37.09 3.51
426 435 1.201424 AAATACCCGAGGTCCTCACC 58.799 55.000 19.15 0.00 44.19 4.02
499 508 2.761559 TCAAAAGATTTCTCACCGCGA 58.238 42.857 8.23 0.00 0.00 5.87
500 509 2.478894 TCAAAAGATTTCTCACCGCGAC 59.521 45.455 8.23 0.00 0.00 5.19
501 510 1.439679 AAAGATTTCTCACCGCGACC 58.560 50.000 8.23 0.00 0.00 4.79
502 511 0.320374 AAGATTTCTCACCGCGACCA 59.680 50.000 8.23 0.00 0.00 4.02
503 512 0.320374 AGATTTCTCACCGCGACCAA 59.680 50.000 8.23 0.00 0.00 3.67
505 514 0.953960 ATTTCTCACCGCGACCAACC 60.954 55.000 8.23 0.00 0.00 3.77
506 515 2.313051 TTTCTCACCGCGACCAACCA 62.313 55.000 8.23 0.00 0.00 3.67
508 517 4.980805 TCACCGCGACCAACCAGC 62.981 66.667 8.23 0.00 0.00 4.85
510 519 4.250305 ACCGCGACCAACCAGCTT 62.250 61.111 8.23 0.00 0.00 3.74
511 520 3.726517 CCGCGACCAACCAGCTTG 61.727 66.667 8.23 0.00 0.00 4.01
513 522 2.639286 GCGACCAACCAGCTTGTG 59.361 61.111 0.00 0.00 0.00 3.33
514 523 2.639286 CGACCAACCAGCTTGTGC 59.361 61.111 0.00 0.00 40.05 4.57
515 524 2.908073 CGACCAACCAGCTTGTGCC 61.908 63.158 0.00 0.00 40.80 5.01
518 527 2.332514 CAACCAGCTTGTGCCACG 59.667 61.111 0.00 0.00 40.80 4.94
520 529 2.480610 AACCAGCTTGTGCCACGTG 61.481 57.895 9.08 9.08 40.80 4.49
521 530 3.663176 CCAGCTTGTGCCACGTGG 61.663 66.667 30.66 30.66 40.80 4.94
531 540 2.268920 CCACGTGGCATAGCTGGT 59.731 61.111 24.02 0.00 0.00 4.00
532 541 1.377202 CCACGTGGCATAGCTGGTT 60.377 57.895 24.02 0.00 0.00 3.67
534 543 0.673333 CACGTGGCATAGCTGGTTGA 60.673 55.000 7.95 0.00 0.00 3.18
535 544 0.673644 ACGTGGCATAGCTGGTTGAC 60.674 55.000 0.00 0.00 0.00 3.18
536 545 1.369091 CGTGGCATAGCTGGTTGACC 61.369 60.000 0.00 0.00 0.00 4.02
537 546 1.078497 TGGCATAGCTGGTTGACCG 60.078 57.895 0.00 0.00 39.43 4.79
538 547 2.472909 GGCATAGCTGGTTGACCGC 61.473 63.158 0.00 8.33 39.43 5.68
539 548 2.472909 GCATAGCTGGTTGACCGCC 61.473 63.158 0.00 0.00 39.43 6.13
540 549 1.819632 CATAGCTGGTTGACCGCCC 60.820 63.158 0.00 0.00 39.43 6.13
541 550 1.995626 ATAGCTGGTTGACCGCCCT 60.996 57.895 0.00 3.76 39.43 5.19
543 552 2.180159 TAGCTGGTTGACCGCCCTTC 62.180 60.000 0.00 0.00 39.43 3.46
544 553 2.429930 CTGGTTGACCGCCCTTCA 59.570 61.111 0.00 0.00 39.43 3.02
546 555 1.303236 TGGTTGACCGCCCTTCATG 60.303 57.895 0.00 0.00 39.43 3.07
547 556 1.303317 GGTTGACCGCCCTTCATGT 60.303 57.895 0.00 0.00 0.00 3.21
548 557 1.586154 GGTTGACCGCCCTTCATGTG 61.586 60.000 0.00 0.00 0.00 3.21
549 558 0.889186 GTTGACCGCCCTTCATGTGT 60.889 55.000 0.00 0.00 0.00 3.72
550 559 0.687920 TTGACCGCCCTTCATGTGTA 59.312 50.000 0.00 0.00 0.00 2.90
551 560 0.249120 TGACCGCCCTTCATGTGTAG 59.751 55.000 0.00 0.00 0.00 2.74
554 563 0.392998 CCGCCCTTCATGTGTAGCTT 60.393 55.000 0.00 0.00 0.00 3.74
555 564 1.134521 CCGCCCTTCATGTGTAGCTTA 60.135 52.381 0.00 0.00 0.00 3.09
557 566 3.206150 CGCCCTTCATGTGTAGCTTAAT 58.794 45.455 0.00 0.00 0.00 1.40
558 567 3.002656 CGCCCTTCATGTGTAGCTTAATG 59.997 47.826 0.00 0.00 0.00 1.90
559 568 3.316308 GCCCTTCATGTGTAGCTTAATGG 59.684 47.826 0.00 0.00 0.00 3.16
560 569 3.885297 CCCTTCATGTGTAGCTTAATGGG 59.115 47.826 0.00 0.00 0.00 4.00
562 571 4.949856 CCTTCATGTGTAGCTTAATGGGTT 59.050 41.667 0.00 0.00 0.00 4.11
563 572 5.418840 CCTTCATGTGTAGCTTAATGGGTTT 59.581 40.000 0.00 0.00 0.00 3.27
564 573 6.601613 CCTTCATGTGTAGCTTAATGGGTTTA 59.398 38.462 0.00 0.00 0.00 2.01
565 574 7.285401 CCTTCATGTGTAGCTTAATGGGTTTAT 59.715 37.037 0.00 0.00 0.00 1.40
567 576 9.860650 TTCATGTGTAGCTTAATGGGTTTATAT 57.139 29.630 0.00 0.00 0.00 0.86
568 577 9.860650 TCATGTGTAGCTTAATGGGTTTATATT 57.139 29.630 0.00 0.00 0.00 1.28
624 633 5.011090 TCTCAAAAGATATGTCACCTCGG 57.989 43.478 0.00 0.00 0.00 4.63
627 636 1.496060 AAGATATGTCACCTCGGCCA 58.504 50.000 2.24 0.00 0.00 5.36
628 637 1.496060 AGATATGTCACCTCGGCCAA 58.504 50.000 2.24 0.00 0.00 4.52
629 638 1.139058 AGATATGTCACCTCGGCCAAC 59.861 52.381 2.24 0.00 0.00 3.77
630 639 0.180406 ATATGTCACCTCGGCCAACC 59.820 55.000 2.24 0.00 0.00 3.77
632 641 2.358737 GTCACCTCGGCCAACCAG 60.359 66.667 2.24 0.00 34.57 4.00
633 642 4.329545 TCACCTCGGCCAACCAGC 62.330 66.667 2.24 0.00 34.57 4.85
634 643 4.335647 CACCTCGGCCAACCAGCT 62.336 66.667 2.24 0.00 34.57 4.24
636 645 3.058160 CCTCGGCCAACCAGCTTG 61.058 66.667 2.24 0.00 34.57 4.01
637 646 3.741476 CTCGGCCAACCAGCTTGC 61.741 66.667 2.24 0.00 34.57 4.01
642 651 4.347453 CCAACCAGCTTGCGCCAC 62.347 66.667 4.18 0.00 36.60 5.01
643 652 4.688419 CAACCAGCTTGCGCCACG 62.688 66.667 4.18 0.00 36.60 4.94
657 666 1.377202 CCACGTGGCATAGCTGGTT 60.377 57.895 24.02 0.00 0.00 3.67
659 668 1.290203 CACGTGGCATAGCTGGTTAG 58.710 55.000 7.95 0.00 0.00 2.34
668 677 2.824489 GCTGGTTAGCCGCCCTTC 60.824 66.667 1.95 0.00 44.33 3.46
669 678 2.668632 CTGGTTAGCCGCCCTTCA 59.331 61.111 0.00 0.00 37.67 3.02
670 679 1.745489 CTGGTTAGCCGCCCTTCAC 60.745 63.158 0.00 0.00 37.67 3.18
671 680 2.818274 GGTTAGCCGCCCTTCACG 60.818 66.667 0.00 0.00 0.00 4.35
672 681 2.047560 GTTAGCCGCCCTTCACGT 60.048 61.111 0.00 0.00 0.00 4.49
674 683 0.179092 GTTAGCCGCCCTTCACGTAT 60.179 55.000 0.00 0.00 0.00 3.06
675 684 1.067516 GTTAGCCGCCCTTCACGTATA 59.932 52.381 0.00 0.00 0.00 1.47
676 685 0.956633 TAGCCGCCCTTCACGTATAG 59.043 55.000 0.00 0.00 0.00 1.31
677 686 1.954651 GCCGCCCTTCACGTATAGC 60.955 63.158 0.00 0.00 0.00 2.97
678 687 1.740285 CCGCCCTTCACGTATAGCT 59.260 57.895 0.00 0.00 0.00 3.32
679 688 0.104304 CCGCCCTTCACGTATAGCTT 59.896 55.000 0.00 0.00 0.00 3.74
680 689 1.338973 CCGCCCTTCACGTATAGCTTA 59.661 52.381 0.00 0.00 0.00 3.09
683 692 3.428870 CGCCCTTCACGTATAGCTTAATG 59.571 47.826 0.00 0.00 0.00 1.90
684 693 3.746492 GCCCTTCACGTATAGCTTAATGG 59.254 47.826 0.00 0.00 0.00 3.16
686 695 4.202326 CCCTTCACGTATAGCTTAATGGGT 60.202 45.833 0.00 0.00 0.00 4.51
687 696 5.365619 CCTTCACGTATAGCTTAATGGGTT 58.634 41.667 0.00 0.00 0.00 4.11
688 697 5.820947 CCTTCACGTATAGCTTAATGGGTTT 59.179 40.000 0.00 0.00 0.00 3.27
689 698 6.987992 CCTTCACGTATAGCTTAATGGGTTTA 59.012 38.462 0.00 0.00 0.00 2.01
727 737 0.108615 ACGGTTGAGCAGATCGAAGG 60.109 55.000 0.00 0.00 0.00 3.46
759 769 0.325671 CAGCTCCCCCTTCTCACCTA 60.326 60.000 0.00 0.00 0.00 3.08
1024 4343 1.523154 TTCCAACGGGAGCATGTTGC 61.523 55.000 0.00 0.00 46.01 4.17
1030 4349 2.484062 GGGAGCATGTTGCCCATCG 61.484 63.158 9.05 0.00 46.52 3.84
1192 4537 1.217244 GACACGGTCGCCCTAATGT 59.783 57.895 0.00 0.00 0.00 2.71
1212 4557 4.386951 CCCATGCCGTCGGTCACA 62.387 66.667 13.94 2.52 0.00 3.58
1352 4724 0.038166 ATTGTCGTGCCCAAGGTGAT 59.962 50.000 0.00 0.00 0.00 3.06
1399 8623 1.447140 GTGAACGTGCCTATGCCGA 60.447 57.895 7.60 0.00 35.82 5.54
1401 8625 0.809636 TGAACGTGCCTATGCCGATG 60.810 55.000 7.60 0.00 35.82 3.84
1487 8767 6.365247 GGTCACGACGCATATATATGTTCTTT 59.635 38.462 21.10 7.67 36.11 2.52
1488 8768 7.539710 GGTCACGACGCATATATATGTTCTTTA 59.460 37.037 21.10 4.42 36.11 1.85
1489 8769 8.363755 GTCACGACGCATATATATGTTCTTTAC 58.636 37.037 21.10 10.99 36.11 2.01
1490 8770 8.077386 TCACGACGCATATATATGTTCTTTACA 58.923 33.333 21.10 1.09 41.97 2.41
1492 8772 8.860128 ACGACGCATATATATGTTCTTTACATG 58.140 33.333 21.10 0.00 46.81 3.21
1493 8773 7.841277 CGACGCATATATATGTTCTTTACATGC 59.159 37.037 21.10 6.60 46.81 4.06
1494 8774 8.546597 ACGCATATATATGTTCTTTACATGCA 57.453 30.769 21.10 0.00 46.81 3.96
1557 8838 7.781548 ACTTTTGTTTACGTCTCAGTGTATT 57.218 32.000 0.00 0.00 0.00 1.89
1591 8872 2.872245 GTTGCTGCTAGTGTTTGACTGA 59.128 45.455 0.00 0.00 35.96 3.41
1743 9028 0.033366 TACAAGCACTGAAGCGAGCA 59.967 50.000 0.00 0.00 40.15 4.26
1744 9029 1.206072 CAAGCACTGAAGCGAGCAC 59.794 57.895 0.00 0.00 40.15 4.40
1838 9123 1.135527 CGTCGTGCTAAGGTCCCATAA 59.864 52.381 0.00 0.00 0.00 1.90
1854 9141 0.541863 ATAAGACCAACGCCCCAGAG 59.458 55.000 0.00 0.00 0.00 3.35
1888 9175 5.300286 CCGCCCATGAAGAGAATTTTAGATT 59.700 40.000 0.00 0.00 0.00 2.40
1919 9206 3.822735 CCAACCTGAAGACACATGAACAT 59.177 43.478 0.00 0.00 0.00 2.71
1986 9273 2.224549 CCGACTAAATCTCGCGAGATCT 59.775 50.000 42.41 34.84 46.75 2.75
2009 9296 1.740285 GAGACACACCTCCACACGT 59.260 57.895 0.00 0.00 0.00 4.49
2038 9325 2.418609 CGATGCTAGACACACCATTGGA 60.419 50.000 10.37 0.00 0.00 3.53
2067 9354 0.546598 AGGCGGGGAGAACCTTATTG 59.453 55.000 0.00 0.00 40.03 1.90
2085 9372 0.321919 TGCATCTTCAAGAAGCCGCT 60.322 50.000 12.00 0.00 38.09 5.52
2102 9389 1.135660 CGCTGCTGTCTCGTCTTCTTA 60.136 52.381 0.00 0.00 0.00 2.10
2117 9404 5.637810 CGTCTTCTTAAGCAGGATACAAACA 59.362 40.000 2.17 0.00 41.41 2.83
2122 9409 9.167311 CTTCTTAAGCAGGATACAAACACTAAT 57.833 33.333 0.00 0.00 41.41 1.73
2145 9432 8.579682 AATAAAACTTGAAGAAGCACATGAAC 57.420 30.769 0.00 0.00 31.68 3.18
2181 9468 3.411517 CAAGGGCCGGGATCCACT 61.412 66.667 15.23 0.08 0.00 4.00
2215 9502 2.688446 CTCTAATGCCACAGGAGACGTA 59.312 50.000 0.00 0.00 0.00 3.57
2290 9580 1.604915 GAGGGACAAAGGGAGGAGC 59.395 63.158 0.00 0.00 0.00 4.70
2291 9581 1.151810 AGGGACAAAGGGAGGAGCA 60.152 57.895 0.00 0.00 0.00 4.26
2292 9582 0.772124 AGGGACAAAGGGAGGAGCAA 60.772 55.000 0.00 0.00 0.00 3.91
2293 9583 0.112412 GGGACAAAGGGAGGAGCAAA 59.888 55.000 0.00 0.00 0.00 3.68
2294 9584 1.480498 GGGACAAAGGGAGGAGCAAAA 60.480 52.381 0.00 0.00 0.00 2.44
2295 9585 1.613925 GGACAAAGGGAGGAGCAAAAC 59.386 52.381 0.00 0.00 0.00 2.43
2296 9586 1.613925 GACAAAGGGAGGAGCAAAACC 59.386 52.381 0.00 0.00 0.00 3.27
2297 9587 1.063266 ACAAAGGGAGGAGCAAAACCA 60.063 47.619 0.00 0.00 0.00 3.67
2298 9588 2.038659 CAAAGGGAGGAGCAAAACCAA 58.961 47.619 0.00 0.00 0.00 3.67
2299 9589 2.433970 CAAAGGGAGGAGCAAAACCAAA 59.566 45.455 0.00 0.00 0.00 3.28
2343 9635 4.320608 TGATTTTGTCAGCCTTTTCACC 57.679 40.909 0.00 0.00 31.80 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.409371 CGCCGTTTTGACTACGTTCTTC 60.409 50.000 0.00 0.00 37.30 2.87
17 18 1.505425 AACCTCGCCGTTTTGACTAC 58.495 50.000 0.00 0.00 0.00 2.73
18 19 2.610232 GGTAACCTCGCCGTTTTGACTA 60.610 50.000 0.00 0.00 0.00 2.59
76 84 6.631016 CATCTCTGGTTGCAAGTAACTAGTA 58.369 40.000 0.00 5.07 39.37 1.82
152 161 0.670854 GTTCTCGGGAAGGTGCACTC 60.671 60.000 17.98 7.21 31.46 3.51
180 189 2.103042 GCGGCTGTCTGGCTTAGTG 61.103 63.158 0.00 0.00 39.32 2.74
181 190 1.831652 AAGCGGCTGTCTGGCTTAGT 61.832 55.000 1.81 0.00 44.58 2.24
183 192 0.611200 TTAAGCGGCTGTCTGGCTTA 59.389 50.000 1.81 0.94 44.58 3.09
197 206 3.694566 CCCCAACCACTAGTCATTTAAGC 59.305 47.826 0.00 0.00 0.00 3.09
201 210 1.613255 CGCCCCAACCACTAGTCATTT 60.613 52.381 0.00 0.00 0.00 2.32
203 212 1.198759 ACGCCCCAACCACTAGTCAT 61.199 55.000 0.00 0.00 0.00 3.06
208 217 2.745037 GTGACGCCCCAACCACTA 59.255 61.111 0.00 0.00 0.00 2.74
209 218 4.265056 GGTGACGCCCCAACCACT 62.265 66.667 0.00 0.00 0.00 4.00
210 219 3.785122 AAGGTGACGCCCCAACCAC 62.785 63.158 0.08 0.00 38.26 4.16
211 220 3.494254 AAGGTGACGCCCCAACCA 61.494 61.111 0.08 0.00 38.26 3.67
213 222 3.670377 GCAAGGTGACGCCCCAAC 61.670 66.667 0.08 0.00 38.26 3.77
233 242 2.358737 AACTTCCCTCAAGCGGCG 60.359 61.111 0.51 0.51 35.17 6.46
234 243 1.600916 ACAACTTCCCTCAAGCGGC 60.601 57.895 0.00 0.00 35.17 6.53
235 244 1.856265 GCACAACTTCCCTCAAGCGG 61.856 60.000 0.00 0.00 35.17 5.52
237 246 1.251251 ATGCACAACTTCCCTCAAGC 58.749 50.000 0.00 0.00 35.17 4.01
238 247 4.012374 ACATATGCACAACTTCCCTCAAG 58.988 43.478 1.58 0.00 38.21 3.02
241 250 5.391312 AAAACATATGCACAACTTCCCTC 57.609 39.130 1.58 0.00 0.00 4.30
242 251 7.480760 AATAAAACATATGCACAACTTCCCT 57.519 32.000 1.58 0.00 0.00 4.20
243 252 8.546597 AAAATAAAACATATGCACAACTTCCC 57.453 30.769 1.58 0.00 0.00 3.97
266 275 7.996644 AGGTGAGGACTCTATGTGTTTTAAAAA 59.003 33.333 1.31 0.00 0.00 1.94
267 276 7.514721 AGGTGAGGACTCTATGTGTTTTAAAA 58.485 34.615 0.00 0.00 0.00 1.52
268 277 7.074653 AGGTGAGGACTCTATGTGTTTTAAA 57.925 36.000 0.56 0.00 0.00 1.52
270 279 6.681729 AAGGTGAGGACTCTATGTGTTTTA 57.318 37.500 0.56 0.00 0.00 1.52
271 280 5.568620 AAGGTGAGGACTCTATGTGTTTT 57.431 39.130 0.56 0.00 0.00 2.43
272 281 5.071788 TGAAAGGTGAGGACTCTATGTGTTT 59.928 40.000 0.56 0.00 0.00 2.83
273 282 4.593206 TGAAAGGTGAGGACTCTATGTGTT 59.407 41.667 0.56 0.00 0.00 3.32
276 285 5.276440 AGATGAAAGGTGAGGACTCTATGT 58.724 41.667 0.56 0.00 0.00 2.29
278 287 7.979786 TTTAGATGAAAGGTGAGGACTCTAT 57.020 36.000 0.56 0.00 0.00 1.98
279 288 7.674348 TCTTTTAGATGAAAGGTGAGGACTCTA 59.326 37.037 0.56 0.00 37.27 2.43
280 289 6.498651 TCTTTTAGATGAAAGGTGAGGACTCT 59.501 38.462 0.56 0.00 37.27 3.24
282 291 6.688073 TCTTTTAGATGAAAGGTGAGGACT 57.312 37.500 0.00 0.00 37.27 3.85
283 292 7.745620 TTTCTTTTAGATGAAAGGTGAGGAC 57.254 36.000 0.00 0.00 37.27 3.85
284 293 8.940397 ATTTTCTTTTAGATGAAAGGTGAGGA 57.060 30.769 0.00 0.00 37.27 3.71
349 358 9.555727 GTTGATAGGCTGAAGTGGTAATTATTA 57.444 33.333 0.00 0.00 0.00 0.98
351 360 7.573710 TGTTGATAGGCTGAAGTGGTAATTAT 58.426 34.615 0.00 0.00 0.00 1.28
352 361 6.953101 TGTTGATAGGCTGAAGTGGTAATTA 58.047 36.000 0.00 0.00 0.00 1.40
354 363 5.435686 TGTTGATAGGCTGAAGTGGTAAT 57.564 39.130 0.00 0.00 0.00 1.89
355 364 4.901197 TGTTGATAGGCTGAAGTGGTAA 57.099 40.909 0.00 0.00 0.00 2.85
359 368 3.120060 GCACTTGTTGATAGGCTGAAGTG 60.120 47.826 0.00 0.00 42.00 3.16
360 369 3.077359 GCACTTGTTGATAGGCTGAAGT 58.923 45.455 0.00 0.00 0.00 3.01
361 370 2.421424 GGCACTTGTTGATAGGCTGAAG 59.579 50.000 0.00 0.00 0.00 3.02
365 374 1.352352 AGTGGCACTTGTTGATAGGCT 59.648 47.619 15.88 0.00 0.00 4.58
366 375 1.826385 AGTGGCACTTGTTGATAGGC 58.174 50.000 15.88 0.00 0.00 3.93
367 376 4.759693 TGTAAAGTGGCACTTGTTGATAGG 59.240 41.667 31.75 0.00 38.66 2.57
369 378 6.000840 TCATGTAAAGTGGCACTTGTTGATA 58.999 36.000 31.75 17.66 38.66 2.15
370 379 4.826733 TCATGTAAAGTGGCACTTGTTGAT 59.173 37.500 31.75 18.69 38.66 2.57
371 380 4.036262 GTCATGTAAAGTGGCACTTGTTGA 59.964 41.667 31.75 25.27 38.66 3.18
375 384 2.228822 GGGTCATGTAAAGTGGCACTTG 59.771 50.000 31.75 20.19 38.66 3.16
376 385 2.108250 AGGGTCATGTAAAGTGGCACTT 59.892 45.455 26.54 26.54 40.80 3.16
377 386 1.705186 AGGGTCATGTAAAGTGGCACT 59.295 47.619 15.88 15.88 28.11 4.40
378 387 2.200373 AGGGTCATGTAAAGTGGCAC 57.800 50.000 10.29 10.29 0.00 5.01
379 388 2.969821 AAGGGTCATGTAAAGTGGCA 57.030 45.000 0.00 0.00 0.00 4.92
405 414 2.026542 GGTGAGGACCTCGGGTATTTTT 60.027 50.000 16.81 0.00 39.47 1.94
406 415 1.558294 GGTGAGGACCTCGGGTATTTT 59.442 52.381 16.81 0.00 39.47 1.82
408 417 2.912020 GGTGAGGACCTCGGGTATT 58.088 57.895 16.81 0.00 39.47 1.89
409 418 4.701286 GGTGAGGACCTCGGGTAT 57.299 61.111 16.81 0.00 39.47 2.73
473 482 6.074356 CGCGGTGAGAAATCTTTTGAATTTTT 60.074 34.615 0.00 0.00 0.00 1.94
474 483 5.402270 CGCGGTGAGAAATCTTTTGAATTTT 59.598 36.000 0.00 0.00 0.00 1.82
475 484 4.917415 CGCGGTGAGAAATCTTTTGAATTT 59.083 37.500 0.00 0.00 0.00 1.82
476 485 4.215399 TCGCGGTGAGAAATCTTTTGAATT 59.785 37.500 6.13 0.00 0.00 2.17
477 486 3.751175 TCGCGGTGAGAAATCTTTTGAAT 59.249 39.130 6.13 0.00 0.00 2.57
478 487 3.059188 GTCGCGGTGAGAAATCTTTTGAA 60.059 43.478 6.13 0.00 0.00 2.69
479 488 2.478894 GTCGCGGTGAGAAATCTTTTGA 59.521 45.455 6.13 0.00 0.00 2.69
480 489 2.412847 GGTCGCGGTGAGAAATCTTTTG 60.413 50.000 6.13 0.00 0.00 2.44
481 490 1.804748 GGTCGCGGTGAGAAATCTTTT 59.195 47.619 6.13 0.00 0.00 2.27
482 491 1.270625 TGGTCGCGGTGAGAAATCTTT 60.271 47.619 6.13 0.00 0.00 2.52
483 492 0.320374 TGGTCGCGGTGAGAAATCTT 59.680 50.000 6.13 0.00 0.00 2.40
484 493 0.320374 TTGGTCGCGGTGAGAAATCT 59.680 50.000 6.13 0.00 0.00 2.40
485 494 0.442699 GTTGGTCGCGGTGAGAAATC 59.557 55.000 6.13 0.00 0.00 2.17
486 495 0.953960 GGTTGGTCGCGGTGAGAAAT 60.954 55.000 6.13 0.00 0.00 2.17
488 497 2.029964 GGTTGGTCGCGGTGAGAA 59.970 61.111 6.13 0.00 0.00 2.87
489 498 3.220999 CTGGTTGGTCGCGGTGAGA 62.221 63.158 6.13 0.00 0.00 3.27
491 500 4.980805 GCTGGTTGGTCGCGGTGA 62.981 66.667 6.13 0.00 0.00 4.02
492 501 4.988598 AGCTGGTTGGTCGCGGTG 62.989 66.667 6.13 0.00 0.00 4.94
493 502 4.250305 AAGCTGGTTGGTCGCGGT 62.250 61.111 6.13 0.00 0.00 5.68
494 503 3.726517 CAAGCTGGTTGGTCGCGG 61.727 66.667 6.13 0.00 31.82 6.46
495 504 2.972505 ACAAGCTGGTTGGTCGCG 60.973 61.111 21.99 0.00 40.90 5.87
496 505 2.639286 CACAAGCTGGTTGGTCGC 59.361 61.111 21.99 0.00 40.90 5.19
499 508 2.127232 GTGGCACAAGCTGGTTGGT 61.127 57.895 21.99 6.68 44.16 3.67
500 509 2.730094 GTGGCACAAGCTGGTTGG 59.270 61.111 21.99 12.63 44.16 3.77
501 510 2.332514 CGTGGCACAAGCTGGTTG 59.667 61.111 19.09 17.29 44.16 3.77
502 511 2.124320 ACGTGGCACAAGCTGGTT 60.124 55.556 19.09 0.00 44.16 3.67
503 512 2.901840 CACGTGGCACAAGCTGGT 60.902 61.111 19.09 2.91 44.16 4.00
514 523 1.377202 AACCAGCTATGCCACGTGG 60.377 57.895 30.66 30.66 38.53 4.94
515 524 0.673333 TCAACCAGCTATGCCACGTG 60.673 55.000 9.08 9.08 0.00 4.49
518 527 1.369091 CGGTCAACCAGCTATGCCAC 61.369 60.000 0.00 0.00 35.14 5.01
520 529 2.472909 GCGGTCAACCAGCTATGCC 61.473 63.158 0.00 0.00 34.38 4.40
521 530 2.472909 GGCGGTCAACCAGCTATGC 61.473 63.158 13.13 2.08 36.36 3.14
522 531 1.819632 GGGCGGTCAACCAGCTATG 60.820 63.158 13.13 0.00 36.36 2.23
524 533 2.180159 GAAGGGCGGTCAACCAGCTA 62.180 60.000 13.13 0.00 36.36 3.32
525 534 3.553095 GAAGGGCGGTCAACCAGCT 62.553 63.158 13.13 0.00 36.36 4.24
526 535 3.056328 GAAGGGCGGTCAACCAGC 61.056 66.667 0.00 4.00 35.72 4.85
527 536 1.002134 ATGAAGGGCGGTCAACCAG 60.002 57.895 0.00 0.00 35.14 4.00
529 538 1.303317 ACATGAAGGGCGGTCAACC 60.303 57.895 0.00 0.00 0.00 3.77
530 539 0.889186 ACACATGAAGGGCGGTCAAC 60.889 55.000 0.00 0.00 0.00 3.18
531 540 0.687920 TACACATGAAGGGCGGTCAA 59.312 50.000 0.00 0.00 0.00 3.18
532 541 0.249120 CTACACATGAAGGGCGGTCA 59.751 55.000 0.00 0.00 0.00 4.02
534 543 1.078426 GCTACACATGAAGGGCGGT 60.078 57.895 0.00 0.00 0.00 5.68
535 544 0.392998 AAGCTACACATGAAGGGCGG 60.393 55.000 0.00 0.00 0.00 6.13
536 545 2.309528 TAAGCTACACATGAAGGGCG 57.690 50.000 0.00 0.00 0.00 6.13
537 546 3.316308 CCATTAAGCTACACATGAAGGGC 59.684 47.826 0.00 0.00 0.00 5.19
538 547 3.885297 CCCATTAAGCTACACATGAAGGG 59.115 47.826 0.00 0.00 0.00 3.95
539 548 4.526970 ACCCATTAAGCTACACATGAAGG 58.473 43.478 0.00 0.00 0.00 3.46
540 549 6.515272 AAACCCATTAAGCTACACATGAAG 57.485 37.500 0.00 0.00 0.00 3.02
541 550 9.860650 ATATAAACCCATTAAGCTACACATGAA 57.139 29.630 0.00 0.00 0.00 2.57
597 606 9.265901 CGAGGTGACATATCTTTTGAGATATTT 57.734 33.333 6.26 1.51 38.90 1.40
599 608 7.382110 CCGAGGTGACATATCTTTTGAGATAT 58.618 38.462 3.66 3.66 40.88 1.63
600 609 6.738731 GCCGAGGTGACATATCTTTTGAGATA 60.739 42.308 0.00 0.00 35.53 1.98
601 610 5.605534 CCGAGGTGACATATCTTTTGAGAT 58.394 41.667 0.00 0.00 0.00 2.75
602 611 4.680708 GCCGAGGTGACATATCTTTTGAGA 60.681 45.833 0.00 0.00 0.00 3.27
603 612 3.557595 GCCGAGGTGACATATCTTTTGAG 59.442 47.826 0.00 0.00 0.00 3.02
606 615 2.238646 TGGCCGAGGTGACATATCTTTT 59.761 45.455 0.00 0.00 0.00 2.27
610 619 1.583054 GTTGGCCGAGGTGACATATC 58.417 55.000 0.00 0.00 0.00 1.63
611 620 0.180406 GGTTGGCCGAGGTGACATAT 59.820 55.000 0.00 0.00 0.00 1.78
612 621 1.195442 TGGTTGGCCGAGGTGACATA 61.195 55.000 0.00 0.00 37.67 2.29
614 623 3.164977 TGGTTGGCCGAGGTGACA 61.165 61.111 0.00 0.00 37.67 3.58
615 624 2.358737 CTGGTTGGCCGAGGTGAC 60.359 66.667 0.00 0.00 37.67 3.67
616 625 4.329545 GCTGGTTGGCCGAGGTGA 62.330 66.667 0.00 0.00 37.67 4.02
617 626 3.850098 AAGCTGGTTGGCCGAGGTG 62.850 63.158 0.00 0.00 37.67 4.00
618 627 3.570212 AAGCTGGTTGGCCGAGGT 61.570 61.111 0.00 0.00 37.67 3.85
619 628 3.058160 CAAGCTGGTTGGCCGAGG 61.058 66.667 11.59 0.00 37.67 4.63
620 629 3.741476 GCAAGCTGGTTGGCCGAG 61.741 66.667 19.87 0.00 36.56 4.63
639 648 0.107897 TAACCAGCTATGCCACGTGG 60.108 55.000 30.66 30.66 38.53 4.94
640 649 1.290203 CTAACCAGCTATGCCACGTG 58.710 55.000 9.08 9.08 0.00 4.49
642 651 2.311294 GCTAACCAGCTATGCCACG 58.689 57.895 0.00 0.00 44.93 4.94
652 661 1.745489 GTGAAGGGCGGCTAACCAG 60.745 63.158 9.56 0.00 34.57 4.00
653 662 2.349755 GTGAAGGGCGGCTAACCA 59.650 61.111 9.56 0.00 34.57 3.67
657 666 0.956633 CTATACGTGAAGGGCGGCTA 59.043 55.000 9.56 0.00 0.00 3.93
659 668 1.954651 GCTATACGTGAAGGGCGGC 60.955 63.158 0.00 0.00 0.00 6.53
660 669 0.104304 AAGCTATACGTGAAGGGCGG 59.896 55.000 0.00 0.00 0.00 6.13
661 670 2.787601 TAAGCTATACGTGAAGGGCG 57.212 50.000 0.00 0.00 0.00 6.13
662 671 3.746492 CCATTAAGCTATACGTGAAGGGC 59.254 47.826 0.00 0.00 0.00 5.19
663 672 4.202326 ACCCATTAAGCTATACGTGAAGGG 60.202 45.833 0.00 0.00 37.43 3.95
665 674 6.920569 AAACCCATTAAGCTATACGTGAAG 57.079 37.500 0.00 0.00 0.00 3.02
666 675 8.832521 CATTAAACCCATTAAGCTATACGTGAA 58.167 33.333 0.00 0.00 36.94 3.18
668 677 7.308348 CCCATTAAACCCATTAAGCTATACGTG 60.308 40.741 0.00 0.00 36.94 4.49
669 678 6.713450 CCCATTAAACCCATTAAGCTATACGT 59.287 38.462 0.00 0.00 36.94 3.57
670 679 6.938030 TCCCATTAAACCCATTAAGCTATACG 59.062 38.462 0.00 0.00 36.94 3.06
671 680 7.094933 CGTCCCATTAAACCCATTAAGCTATAC 60.095 40.741 0.00 0.00 36.94 1.47
672 681 6.938030 CGTCCCATTAAACCCATTAAGCTATA 59.062 38.462 0.00 0.00 36.94 1.31
674 683 5.104444 TCGTCCCATTAAACCCATTAAGCTA 60.104 40.000 0.00 0.00 36.94 3.32
675 684 3.951680 CGTCCCATTAAACCCATTAAGCT 59.048 43.478 0.00 0.00 36.94 3.74
676 685 3.949113 TCGTCCCATTAAACCCATTAAGC 59.051 43.478 0.00 0.00 36.94 3.09
677 686 6.709018 ATTCGTCCCATTAAACCCATTAAG 57.291 37.500 0.00 0.00 36.94 1.85
678 687 8.770010 ATTATTCGTCCCATTAAACCCATTAA 57.230 30.769 0.00 0.00 37.86 1.40
679 688 7.999545 TGATTATTCGTCCCATTAAACCCATTA 59.000 33.333 0.00 0.00 0.00 1.90
680 689 6.836527 TGATTATTCGTCCCATTAAACCCATT 59.163 34.615 0.00 0.00 0.00 3.16
683 692 6.544564 TCTTGATTATTCGTCCCATTAAACCC 59.455 38.462 0.00 0.00 0.00 4.11
684 693 7.415229 GTCTTGATTATTCGTCCCATTAAACC 58.585 38.462 0.00 0.00 0.00 3.27
686 695 6.259167 CCGTCTTGATTATTCGTCCCATTAAA 59.741 38.462 0.00 0.00 0.00 1.52
687 696 5.756347 CCGTCTTGATTATTCGTCCCATTAA 59.244 40.000 0.00 0.00 0.00 1.40
688 697 5.163385 ACCGTCTTGATTATTCGTCCCATTA 60.163 40.000 0.00 0.00 0.00 1.90
689 698 4.127171 CCGTCTTGATTATTCGTCCCATT 58.873 43.478 0.00 0.00 0.00 3.16
997 4310 2.035626 CCCGTTGGAAGCCATGGT 59.964 61.111 14.67 0.00 31.53 3.55
1030 4349 4.152625 GAGCACGCACGCCATGAC 62.153 66.667 0.00 0.00 0.00 3.06
1183 4526 1.109323 GGCATGGGTGACATTAGGGC 61.109 60.000 0.00 0.00 37.84 5.19
1188 4533 1.745115 CGACGGCATGGGTGACATT 60.745 57.895 0.00 0.00 37.84 2.71
1192 4537 4.077184 GACCGACGGCATGGGTGA 62.077 66.667 15.39 0.00 40.04 4.02
1331 4703 1.303317 ACCTTGGGCACGACAATCC 60.303 57.895 0.00 0.00 0.00 3.01
1487 8767 1.522668 AACGCAGAGCTTTGCATGTA 58.477 45.000 26.79 0.00 44.28 2.29
1488 8768 0.670162 AAACGCAGAGCTTTGCATGT 59.330 45.000 26.79 15.63 44.28 3.21
1489 8769 1.774639 AAAACGCAGAGCTTTGCATG 58.225 45.000 26.79 15.01 44.28 4.06
1490 8770 3.568538 CTTAAAACGCAGAGCTTTGCAT 58.431 40.909 26.79 11.31 44.28 3.96
1491 8771 2.858260 GCTTAAAACGCAGAGCTTTGCA 60.858 45.455 26.79 6.09 44.28 4.08
1492 8772 1.716050 GCTTAAAACGCAGAGCTTTGC 59.284 47.619 18.90 18.90 40.67 3.68
1493 8773 1.971962 CGCTTAAAACGCAGAGCTTTG 59.028 47.619 0.00 0.00 33.09 2.77
1494 8774 1.602377 ACGCTTAAAACGCAGAGCTTT 59.398 42.857 0.00 0.00 33.09 3.51
1557 8838 7.444183 ACACTAGCAGCAACAGACTAAAAATAA 59.556 33.333 0.00 0.00 0.00 1.40
1562 8843 4.336889 ACACTAGCAGCAACAGACTAAA 57.663 40.909 0.00 0.00 0.00 1.85
1633 8915 7.743400 CCATGATTGAAGATGAATAAATCGACG 59.257 37.037 0.00 0.00 31.33 5.12
1838 9123 4.021925 GCTCTGGGGCGTTGGTCT 62.022 66.667 0.00 0.00 0.00 3.85
1869 9156 9.182214 TCCTTCCAATCTAAAATTCTCTTCATG 57.818 33.333 0.00 0.00 0.00 3.07
1919 9206 2.165030 GGATCCGGTCTTTGTTCGTCTA 59.835 50.000 0.00 0.00 0.00 2.59
1986 9273 3.311110 GGAGGTGTGTCTCCGGCA 61.311 66.667 0.00 0.00 43.19 5.69
2009 9296 0.107361 TGTCTAGCATCGTCGGAGGA 60.107 55.000 2.53 2.53 0.00 3.71
2067 9354 0.098376 CAGCGGCTTCTTGAAGATGC 59.902 55.000 20.86 20.86 42.61 3.91
2085 9372 2.296190 TGCTTAAGAAGACGAGACAGCA 59.704 45.455 6.67 0.00 33.69 4.41
2102 9389 9.297037 AGTTTTATTAGTGTTTGTATCCTGCTT 57.703 29.630 0.00 0.00 0.00 3.91
2117 9404 9.066892 TCATGTGCTTCTTCAAGTTTTATTAGT 57.933 29.630 0.00 0.00 31.45 2.24
2122 9409 6.972328 GTGTTCATGTGCTTCTTCAAGTTTTA 59.028 34.615 0.00 0.00 31.45 1.52
2195 9482 1.557099 ACGTCTCCTGTGGCATTAGA 58.443 50.000 0.00 0.00 0.00 2.10
2200 9487 0.965866 CTCCTACGTCTCCTGTGGCA 60.966 60.000 0.00 0.00 0.00 4.92
2242 9529 2.269241 GCGGCTAGGGTTTCTGCT 59.731 61.111 0.00 0.00 0.00 4.24
2343 9635 6.901887 GTGTGCATGTTCGATTAATCAGTTAG 59.098 38.462 15.57 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.