Multiple sequence alignment - TraesCS2B01G550100

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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 TraesCS2B01G550100 chr2B 100.000 3221 0 0 1 3221 746079418 746082638 0.000000e+00 5949
1 TraesCS2B01G550100 chr2B 88.889 783 51 17 851 1620 746105294 746106053 0.000000e+00 931
2 TraesCS2B01G550100 chr2B 79.396 364 52 13 493 850 107120135 107119789 5.370000e-58 235
3 TraesCS2B01G550100 chr2B 76.483 472 74 20 383 849 685734378 685734817 4.180000e-54 222
4 TraesCS2B01G550100 chr2B 94.444 126 3 3 3096 3221 344425537 344425658 1.180000e-44 191
5 TraesCS2B01G550100 chr2D 88.699 2106 132 39 344 2406 611216134 611214092 0.000000e+00 2473
6 TraesCS2B01G550100 chr2D 87.009 331 31 10 1 322 649368316 649368643 2.360000e-96 363
7 TraesCS2B01G550100 chr2D 84.962 133 16 4 492 622 491492399 491492529 7.250000e-27 132
8 TraesCS2B01G550100 chr7B 91.713 712 57 2 2402 3112 726288911 726288201 0.000000e+00 987
9 TraesCS2B01G550100 chr7B 87.009 331 29 9 1 322 718954510 718954835 8.490000e-96 361
10 TraesCS2B01G550100 chr5D 90.469 703 58 6 2412 3113 500151038 500151732 0.000000e+00 918
11 TraesCS2B01G550100 chr5D 86.707 331 34 5 1 322 14644974 14645303 3.060000e-95 359
12 TraesCS2B01G550100 chr5D 86.970 330 30 10 1 322 454029730 454030054 3.060000e-95 359
13 TraesCS2B01G550100 chr3A 90.327 703 62 4 2412 3113 8943718 8943021 0.000000e+00 917
14 TraesCS2B01G550100 chr3A 88.592 710 75 4 2405 3113 74788442 74787738 0.000000e+00 857
15 TraesCS2B01G550100 chr3A 99.083 109 1 0 3113 3221 398514964 398514856 2.540000e-46 196
16 TraesCS2B01G550100 chr3A 77.635 389 42 20 490 847 617924389 617924763 9.120000e-46 195
17 TraesCS2B01G550100 chr6D 89.758 703 64 6 2412 3113 456099622 456100317 0.000000e+00 893
18 TraesCS2B01G550100 chr6D 84.884 258 34 3 344 598 418309436 418309181 4.120000e-64 255
19 TraesCS2B01G550100 chr6D 78.392 398 37 22 490 847 77679346 77678958 2.520000e-51 213
20 TraesCS2B01G550100 chr6D 81.517 211 28 6 344 551 431068142 431067940 2.570000e-36 163
21 TraesCS2B01G550100 chr7D 89.474 703 68 4 2412 3113 553066044 553065347 0.000000e+00 883
22 TraesCS2B01G550100 chr7D 87.311 331 30 9 1 322 119561180 119561507 5.080000e-98 368
23 TraesCS2B01G550100 chr7D 87.135 171 19 2 344 512 4698111 4697942 1.180000e-44 191
24 TraesCS2B01G550100 chr7D 83.333 192 22 9 344 533 638594036 638594219 5.530000e-38 169
25 TraesCS2B01G550100 chr5B 89.205 704 63 6 2411 3113 586399780 586400471 0.000000e+00 867
26 TraesCS2B01G550100 chr5B 81.343 536 74 16 1 512 604173581 604174114 2.310000e-111 412
27 TraesCS2B01G550100 chr5B 95.122 123 6 0 3099 3221 656485305 656485427 9.120000e-46 195
28 TraesCS2B01G550100 chr6A 88.636 704 74 4 2411 3113 27628139 27628837 0.000000e+00 852
29 TraesCS2B01G550100 chr6A 86.810 326 34 8 3 321 228540193 228540516 3.950000e-94 355
30 TraesCS2B01G550100 chr6A 79.808 520 64 16 344 849 33030315 33030807 1.110000e-89 340
31 TraesCS2B01G550100 chr4A 88.352 704 76 4 2411 3113 470140188 470139490 0.000000e+00 841
32 TraesCS2B01G550100 chr4A 95.082 122 6 0 3100 3221 320718184 320718063 3.280000e-45 193
33 TraesCS2B01G550100 chr1D 81.214 527 66 13 343 847 58617091 58616576 8.380000e-106 394
34 TraesCS2B01G550100 chr1D 87.898 157 16 2 692 847 6668076 6668230 7.100000e-42 182
35 TraesCS2B01G550100 chr4D 86.747 332 31 7 1 321 69220008 69219679 1.100000e-94 357
36 TraesCS2B01G550100 chr3D 86.364 330 34 8 1 322 89631657 89631983 1.840000e-92 350
37 TraesCS2B01G550100 chr3D 79.028 391 49 17 490 850 8466990 8466603 1.490000e-58 237
38 TraesCS2B01G550100 chr1B 78.244 524 62 19 343 849 416635196 416635684 4.070000e-74 289
39 TraesCS2B01G550100 chr7A 84.490 245 30 5 354 598 8904139 8903903 5.370000e-58 235
40 TraesCS2B01G550100 chr7A 85.965 171 19 5 346 512 647293461 647293292 9.180000e-41 178
41 TraesCS2B01G550100 chr7A 85.030 167 22 3 684 847 624800308 624800142 1.990000e-37 167
42 TraesCS2B01G550100 chr5A 78.643 398 45 18 493 854 28657035 28656642 8.990000e-56 228
43 TraesCS2B01G550100 chr5A 85.714 161 18 4 692 847 523931215 523931375 7.150000e-37 165
44 TraesCS2B01G550100 chr6B 99.099 111 1 0 3111 3221 173296945 173297055 1.960000e-47 200
45 TraesCS2B01G550100 chr6B 99.099 111 1 0 3111 3221 480497692 480497582 1.960000e-47 200
46 TraesCS2B01G550100 chr3B 99.099 111 1 0 3111 3221 203917714 203917604 1.960000e-47 200
47 TraesCS2B01G550100 chr3B 97.391 115 3 0 3107 3221 141597122 141597008 2.540000e-46 196
48 TraesCS2B01G550100 chr3B 86.747 166 18 3 344 507 776995307 776995144 7.100000e-42 182
49 TraesCS2B01G550100 chr2A 94.355 124 7 0 3098 3221 279892761 279892638 1.180000e-44 191
50 TraesCS2B01G550100 chr2A 87.302 126 11 4 490 612 183541183 183541060 4.330000e-29 139
51 TraesCS2B01G550100 chr2A 96.875 64 2 0 869 932 743548169 743548106 1.220000e-19 108


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 TraesCS2B01G550100 chr2B 746079418 746082638 3220 False 5949 5949 100.000 1 3221 1 chr2B.!!$F3 3220
1 TraesCS2B01G550100 chr2B 746105294 746106053 759 False 931 931 88.889 851 1620 1 chr2B.!!$F4 769
2 TraesCS2B01G550100 chr2D 611214092 611216134 2042 True 2473 2473 88.699 344 2406 1 chr2D.!!$R1 2062
3 TraesCS2B01G550100 chr7B 726288201 726288911 710 True 987 987 91.713 2402 3112 1 chr7B.!!$R1 710
4 TraesCS2B01G550100 chr5D 500151038 500151732 694 False 918 918 90.469 2412 3113 1 chr5D.!!$F3 701
5 TraesCS2B01G550100 chr3A 8943021 8943718 697 True 917 917 90.327 2412 3113 1 chr3A.!!$R1 701
6 TraesCS2B01G550100 chr3A 74787738 74788442 704 True 857 857 88.592 2405 3113 1 chr3A.!!$R2 708
7 TraesCS2B01G550100 chr6D 456099622 456100317 695 False 893 893 89.758 2412 3113 1 chr6D.!!$F1 701
8 TraesCS2B01G550100 chr7D 553065347 553066044 697 True 883 883 89.474 2412 3113 1 chr7D.!!$R2 701
9 TraesCS2B01G550100 chr5B 586399780 586400471 691 False 867 867 89.205 2411 3113 1 chr5B.!!$F1 702
10 TraesCS2B01G550100 chr5B 604173581 604174114 533 False 412 412 81.343 1 512 1 chr5B.!!$F2 511
11 TraesCS2B01G550100 chr6A 27628139 27628837 698 False 852 852 88.636 2411 3113 1 chr6A.!!$F1 702
12 TraesCS2B01G550100 chr4A 470139490 470140188 698 True 841 841 88.352 2411 3113 1 chr4A.!!$R2 702
13 TraesCS2B01G550100 chr1D 58616576 58617091 515 True 394 394 81.214 343 847 1 chr1D.!!$R1 504

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
211 216 0.036952 CAAGGCACGACCATGACTCT 60.037 55.0 0.0 0.0 36.73 3.24 F
818 1062 0.103937 GCTGATAGTTGCGAGGCTCT 59.896 55.0 13.5 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2081 0.318441 TGGACTCGACTTTGCTCAGG 59.682 55.0 0.00 0.00 0.0 3.86 R
2240 2503 0.324943 AAGGTCATGCGTGGCTACTT 59.675 50.0 10.92 3.31 0.0 2.24 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
90 95 3.982576 TTTCCTTTTCGAAAGAGGCAC 57.017 42.857 23.34 0.00 43.69 5.01
93 98 0.110192 CTTTTCGAAAGAGGCACGCC 60.110 55.000 10.98 0.00 43.69 5.68
118 123 2.622942 GCCTCTCACAAAATCACAACCA 59.377 45.455 0.00 0.00 0.00 3.67
120 125 4.458989 GCCTCTCACAAAATCACAACCATA 59.541 41.667 0.00 0.00 0.00 2.74
126 131 6.068010 TCACAAAATCACAACCATACCTCTT 58.932 36.000 0.00 0.00 0.00 2.85
127 132 6.549364 TCACAAAATCACAACCATACCTCTTT 59.451 34.615 0.00 0.00 0.00 2.52
130 135 3.328382 TCACAACCATACCTCTTTCGG 57.672 47.619 0.00 0.00 0.00 4.30
200 205 2.196295 TTTTTCGTTTCCAAGGCACG 57.804 45.000 4.77 4.77 35.18 5.34
201 206 1.380524 TTTTCGTTTCCAAGGCACGA 58.619 45.000 8.67 8.67 41.05 4.35
202 207 0.658897 TTTCGTTTCCAAGGCACGAC 59.341 50.000 11.41 0.00 42.40 4.34
203 208 1.161563 TTCGTTTCCAAGGCACGACC 61.162 55.000 11.41 0.00 42.40 4.79
204 209 1.890041 CGTTTCCAAGGCACGACCA 60.890 57.895 5.10 0.00 43.14 4.02
205 210 1.234615 CGTTTCCAAGGCACGACCAT 61.235 55.000 5.10 0.00 43.14 3.55
206 211 0.240945 GTTTCCAAGGCACGACCATG 59.759 55.000 0.00 0.00 43.14 3.66
207 212 0.109532 TTTCCAAGGCACGACCATGA 59.890 50.000 0.00 0.00 39.64 3.07
208 213 0.605319 TTCCAAGGCACGACCATGAC 60.605 55.000 0.00 0.00 39.64 3.06
209 214 1.003355 CCAAGGCACGACCATGACT 60.003 57.895 0.00 0.00 40.83 3.41
210 215 1.021390 CCAAGGCACGACCATGACTC 61.021 60.000 0.00 0.00 36.73 3.36
211 216 0.036952 CAAGGCACGACCATGACTCT 60.037 55.000 0.00 0.00 36.73 3.24
212 217 0.247736 AAGGCACGACCATGACTCTC 59.752 55.000 0.00 0.00 36.73 3.20
213 218 1.517257 GGCACGACCATGACTCTCG 60.517 63.158 0.00 0.00 38.86 4.04
214 219 1.506718 GCACGACCATGACTCTCGA 59.493 57.895 0.00 0.00 0.00 4.04
215 220 0.524392 GCACGACCATGACTCTCGAG 60.524 60.000 5.93 5.93 0.00 4.04
216 221 1.087501 CACGACCATGACTCTCGAGA 58.912 55.000 15.70 15.70 0.00 4.04
217 222 1.468914 CACGACCATGACTCTCGAGAA 59.531 52.381 17.36 1.60 0.00 2.87
218 223 2.095212 CACGACCATGACTCTCGAGAAA 60.095 50.000 17.36 5.59 0.00 2.52
219 224 2.162608 ACGACCATGACTCTCGAGAAAG 59.837 50.000 17.36 8.39 0.00 2.62
220 225 2.535331 GACCATGACTCTCGAGAAAGC 58.465 52.381 17.36 9.04 0.00 3.51
221 226 1.895798 ACCATGACTCTCGAGAAAGCA 59.104 47.619 17.36 14.33 0.00 3.91
222 227 2.266554 CCATGACTCTCGAGAAAGCAC 58.733 52.381 17.36 6.79 0.00 4.40
223 228 2.353109 CCATGACTCTCGAGAAAGCACA 60.353 50.000 17.36 11.87 0.00 4.57
224 229 3.320626 CATGACTCTCGAGAAAGCACAA 58.679 45.455 17.36 0.00 0.00 3.33
225 230 2.743938 TGACTCTCGAGAAAGCACAAC 58.256 47.619 17.36 2.84 0.00 3.32
226 231 2.062519 GACTCTCGAGAAAGCACAACC 58.937 52.381 17.36 0.00 0.00 3.77
227 232 1.063806 CTCTCGAGAAAGCACAACCG 58.936 55.000 17.36 0.00 0.00 4.44
228 233 0.387929 TCTCGAGAAAGCACAACCGT 59.612 50.000 14.01 0.00 0.00 4.83
229 234 0.508641 CTCGAGAAAGCACAACCGTG 59.491 55.000 6.58 0.00 46.56 4.94
237 242 3.414700 CACAACCGTGCCTCTCGC 61.415 66.667 0.00 0.00 36.06 5.03
256 261 2.619013 CGGAAGCAAAACCATGACTC 57.381 50.000 0.00 0.00 0.00 3.36
257 262 2.154462 CGGAAGCAAAACCATGACTCT 58.846 47.619 0.00 0.00 0.00 3.24
258 263 2.160417 CGGAAGCAAAACCATGACTCTC 59.840 50.000 0.00 0.00 0.00 3.20
259 264 2.160417 GGAAGCAAAACCATGACTCTCG 59.840 50.000 0.00 0.00 0.00 4.04
260 265 2.550830 AGCAAAACCATGACTCTCGT 57.449 45.000 0.00 0.00 0.00 4.18
261 266 2.146342 AGCAAAACCATGACTCTCGTG 58.854 47.619 0.00 0.00 33.30 4.35
262 267 2.143122 GCAAAACCATGACTCTCGTGA 58.857 47.619 0.00 0.00 35.46 4.35
263 268 2.548057 GCAAAACCATGACTCTCGTGAA 59.452 45.455 0.00 0.00 35.46 3.18
264 269 3.003275 GCAAAACCATGACTCTCGTGAAA 59.997 43.478 0.00 0.00 35.46 2.69
265 270 4.776743 CAAAACCATGACTCTCGTGAAAG 58.223 43.478 0.00 0.00 35.46 2.62
266 271 4.336889 AAACCATGACTCTCGTGAAAGA 57.663 40.909 0.00 0.00 35.46 2.52
267 272 4.336889 AACCATGACTCTCGTGAAAGAA 57.663 40.909 0.00 0.00 35.46 2.52
268 273 4.336889 ACCATGACTCTCGTGAAAGAAA 57.663 40.909 0.00 0.00 35.46 2.52
269 274 4.703897 ACCATGACTCTCGTGAAAGAAAA 58.296 39.130 0.00 0.00 35.46 2.29
270 275 5.123227 ACCATGACTCTCGTGAAAGAAAAA 58.877 37.500 0.00 0.00 35.46 1.94
310 315 3.430333 TTTTTCGTTTCCAAGAGGCAC 57.570 42.857 0.00 0.00 33.74 5.01
311 316 0.941542 TTTCGTTTCCAAGAGGCACG 59.058 50.000 0.00 0.00 40.61 5.34
312 317 0.105224 TTCGTTTCCAAGAGGCACGA 59.895 50.000 0.00 5.13 43.95 4.35
313 318 0.599204 TCGTTTCCAAGAGGCACGAC 60.599 55.000 0.00 0.00 42.09 4.34
314 319 0.878523 CGTTTCCAAGAGGCACGACA 60.879 55.000 0.00 0.00 41.32 4.35
315 320 0.868406 GTTTCCAAGAGGCACGACAG 59.132 55.000 0.00 0.00 33.74 3.51
316 321 0.468226 TTTCCAAGAGGCACGACAGT 59.532 50.000 0.00 0.00 33.74 3.55
327 332 3.111405 ACGACAGTGACTCCTGTGA 57.889 52.632 0.00 0.00 45.46 3.58
328 333 0.669077 ACGACAGTGACTCCTGTGAC 59.331 55.000 0.00 0.00 45.46 3.67
329 334 0.955178 CGACAGTGACTCCTGTGACT 59.045 55.000 0.00 0.00 45.46 3.41
330 335 1.068885 CGACAGTGACTCCTGTGACTC 60.069 57.143 0.00 0.00 45.46 3.36
331 336 2.235016 GACAGTGACTCCTGTGACTCT 58.765 52.381 0.00 0.00 45.46 3.24
332 337 2.625790 GACAGTGACTCCTGTGACTCTT 59.374 50.000 0.00 0.00 45.46 2.85
333 338 2.363680 ACAGTGACTCCTGTGACTCTTG 59.636 50.000 0.00 0.00 43.86 3.02
334 339 2.625314 CAGTGACTCCTGTGACTCTTGA 59.375 50.000 0.00 0.00 38.55 3.02
335 340 3.257873 CAGTGACTCCTGTGACTCTTGAT 59.742 47.826 0.00 0.00 38.55 2.57
336 341 3.900601 AGTGACTCCTGTGACTCTTGATT 59.099 43.478 0.00 0.00 35.83 2.57
337 342 4.346418 AGTGACTCCTGTGACTCTTGATTT 59.654 41.667 0.00 0.00 35.83 2.17
338 343 5.059833 GTGACTCCTGTGACTCTTGATTTT 58.940 41.667 0.00 0.00 0.00 1.82
339 344 5.529060 GTGACTCCTGTGACTCTTGATTTTT 59.471 40.000 0.00 0.00 0.00 1.94
380 385 1.006281 TCATTTCCAAGAGGCATGGCT 59.994 47.619 23.58 23.58 37.88 4.75
397 402 0.664767 GCTGTGACTCTCGCGAAAGT 60.665 55.000 16.32 16.32 0.00 2.66
411 416 1.798813 CGAAAGTACAACTGTGCCTCC 59.201 52.381 0.00 0.00 0.00 4.30
509 732 3.491581 GTGACTCTCGCGAAAGGAA 57.508 52.632 14.96 0.00 0.00 3.36
510 733 1.779569 GTGACTCTCGCGAAAGGAAA 58.220 50.000 14.96 0.00 0.00 3.13
511 734 2.132762 GTGACTCTCGCGAAAGGAAAA 58.867 47.619 14.96 0.00 0.00 2.29
512 735 2.155924 GTGACTCTCGCGAAAGGAAAAG 59.844 50.000 14.96 0.00 0.00 2.27
513 736 2.035449 TGACTCTCGCGAAAGGAAAAGA 59.965 45.455 14.96 2.20 0.00 2.52
514 737 3.057734 GACTCTCGCGAAAGGAAAAGAA 58.942 45.455 14.96 0.00 0.00 2.52
515 738 2.801111 ACTCTCGCGAAAGGAAAAGAAC 59.199 45.455 14.96 0.00 0.00 3.01
516 739 3.060602 CTCTCGCGAAAGGAAAAGAACT 58.939 45.455 11.33 0.00 0.00 3.01
517 740 2.800544 TCTCGCGAAAGGAAAAGAACTG 59.199 45.455 11.33 0.00 0.00 3.16
518 741 2.800544 CTCGCGAAAGGAAAAGAACTGA 59.199 45.455 11.33 0.00 0.00 3.41
519 742 3.199677 TCGCGAAAGGAAAAGAACTGAA 58.800 40.909 6.20 0.00 0.00 3.02
520 743 3.623960 TCGCGAAAGGAAAAGAACTGAAA 59.376 39.130 6.20 0.00 0.00 2.69
521 744 4.095185 TCGCGAAAGGAAAAGAACTGAAAA 59.905 37.500 6.20 0.00 0.00 2.29
522 745 4.204370 CGCGAAAGGAAAAGAACTGAAAAC 59.796 41.667 0.00 0.00 0.00 2.43
523 746 5.099575 GCGAAAGGAAAAGAACTGAAAACA 58.900 37.500 0.00 0.00 0.00 2.83
524 747 5.004440 GCGAAAGGAAAAGAACTGAAAACAC 59.996 40.000 0.00 0.00 0.00 3.32
525 748 6.322491 CGAAAGGAAAAGAACTGAAAACACT 58.678 36.000 0.00 0.00 0.00 3.55
526 749 6.806739 CGAAAGGAAAAGAACTGAAAACACTT 59.193 34.615 0.00 0.00 0.00 3.16
527 750 7.328493 CGAAAGGAAAAGAACTGAAAACACTTT 59.672 33.333 0.00 0.00 33.18 2.66
528 751 7.889589 AAGGAAAAGAACTGAAAACACTTTG 57.110 32.000 0.00 0.00 32.36 2.77
529 752 6.993079 AGGAAAAGAACTGAAAACACTTTGT 58.007 32.000 0.00 0.00 32.36 2.83
530 753 7.441836 AGGAAAAGAACTGAAAACACTTTGTT 58.558 30.769 0.00 0.00 43.41 2.83
566 789 3.295273 ACGGCTGTGACTCTCGCA 61.295 61.111 0.00 0.00 35.36 5.10
586 809 3.769536 CAAAAGCAAAACCGTGACTCTT 58.230 40.909 0.00 0.00 0.00 2.85
592 815 3.506810 CAAAACCGTGACTCTTGCAAAA 58.493 40.909 0.00 0.00 0.00 2.44
593 816 3.420839 AAACCGTGACTCTTGCAAAAG 57.579 42.857 0.00 0.00 0.00 2.27
594 817 2.038387 ACCGTGACTCTTGCAAAAGT 57.962 45.000 4.77 4.77 0.00 2.66
595 818 3.188159 ACCGTGACTCTTGCAAAAGTA 57.812 42.857 5.16 0.00 0.00 2.24
596 819 3.537580 ACCGTGACTCTTGCAAAAGTAA 58.462 40.909 5.16 0.00 0.00 2.24
696 937 5.933790 GTGGAAAACCAAAACCAGAAAAAC 58.066 37.500 0.00 0.00 32.89 2.43
697 938 5.004448 TGGAAAACCAAAACCAGAAAAACC 58.996 37.500 0.00 0.00 0.00 3.27
698 939 4.093703 GGAAAACCAAAACCAGAAAAACCG 59.906 41.667 0.00 0.00 0.00 4.44
700 941 1.828595 ACCAAAACCAGAAAAACCGCT 59.171 42.857 0.00 0.00 0.00 5.52
709 953 3.491792 CCAGAAAAACCGCTAAAAAGCCA 60.492 43.478 0.00 0.00 0.00 4.75
714 958 6.317642 AGAAAAACCGCTAAAAAGCCAAAAAT 59.682 30.769 0.00 0.00 0.00 1.82
720 964 3.247411 GCTAAAAAGCCAAAAATGCGTGT 59.753 39.130 0.00 0.00 0.00 4.49
733 977 7.698130 CCAAAAATGCGTGTGGAAAAATAAAAA 59.302 29.630 0.00 0.00 32.54 1.94
755 999 1.394917 CAAAATCTGAAGGGAGCGTCG 59.605 52.381 0.00 0.00 0.00 5.12
788 1032 2.510238 GCGAATGGCTGAGAGCGT 60.510 61.111 0.00 0.00 43.62 5.07
818 1062 0.103937 GCTGATAGTTGCGAGGCTCT 59.896 55.000 13.50 0.00 0.00 4.09
864 1108 3.644953 CTCCCCTTTAGGAGCTCCT 57.355 57.895 36.62 36.62 46.76 3.69
865 1109 2.777459 CTCCCCTTTAGGAGCTCCTA 57.223 55.000 34.33 34.33 46.76 2.94
886 1130 3.118531 AGGGGATCTCTGTTACTTGCAT 58.881 45.455 0.00 0.00 0.00 3.96
890 1134 4.051922 GGATCTCTGTTACTTGCATACGG 58.948 47.826 0.00 0.00 0.00 4.02
913 1157 6.415573 GGAACCCTAATATAAGTGGGCTATG 58.584 44.000 0.00 0.00 43.25 2.23
929 1179 2.456364 TGGAGGCCCATCTCACCT 59.544 61.111 0.00 0.00 37.58 4.00
930 1180 1.709711 TGGAGGCCCATCTCACCTA 59.290 57.895 0.00 0.00 37.58 3.08
1082 1339 1.202879 ACGAATCCAGCCCTTCAAACA 60.203 47.619 0.00 0.00 0.00 2.83
1089 1346 1.007387 GCCCTTCAAACACCAAGCG 60.007 57.895 0.00 0.00 0.00 4.68
1134 1391 1.893808 CAACTCGTGCCTGGTGCTT 60.894 57.895 0.00 0.00 42.00 3.91
1216 1473 3.634397 ACAGGTCCATCATCGTTCATT 57.366 42.857 0.00 0.00 0.00 2.57
1223 1480 5.506317 GGTCCATCATCGTTCATTTTCATCC 60.506 44.000 0.00 0.00 0.00 3.51
1224 1481 5.066375 GTCCATCATCGTTCATTTTCATCCA 59.934 40.000 0.00 0.00 0.00 3.41
1233 1490 1.376609 ATTTTCATCCACTCGCCGGC 61.377 55.000 19.07 19.07 0.00 6.13
1238 1495 3.521529 ATCCACTCGCCGGCTATGC 62.522 63.158 26.68 0.00 0.00 3.14
1250 1507 0.459237 GGCTATGCCGATCGATCTGG 60.459 60.000 22.43 23.04 39.62 3.86
1261 1518 2.121538 CGATCTGGCCGAGTCCTGA 61.122 63.158 0.00 0.00 38.24 3.86
1267 1524 0.472471 TGGCCGAGTCCTGAGTTTTT 59.528 50.000 0.00 0.00 0.00 1.94
1449 1709 1.004440 GAGTGGAAGAAGCACGGCT 60.004 57.895 0.00 0.00 42.56 5.52
1514 1777 1.248785 CGTTCGTCCTGAAGAGGGGA 61.249 60.000 0.00 0.00 40.25 4.81
1522 1785 0.391793 CTGAAGAGGGGAAAGGCGTC 60.392 60.000 0.00 0.00 0.00 5.19
1713 1976 3.050275 GTGGAGCTGGGCGACAAC 61.050 66.667 0.00 0.00 0.00 3.32
1723 1986 1.566077 GGCGACAACGTGTACCAAC 59.434 57.895 0.00 0.00 41.98 3.77
1726 1989 1.332552 GCGACAACGTGTACCAACAAG 60.333 52.381 0.00 0.00 40.48 3.16
1731 1994 3.132646 ACAACGTGTACCAACAAGTCCTA 59.867 43.478 0.00 0.00 45.85 2.94
1736 1999 4.158025 CGTGTACCAACAAGTCCTAGAGAT 59.842 45.833 0.00 0.00 37.36 2.75
1744 2007 1.404843 AGTCCTAGAGATGCCGTTCC 58.595 55.000 0.00 0.00 0.00 3.62
1754 2017 2.202453 GCCGTTCCTCGACGAGAC 60.202 66.667 26.11 15.57 45.47 3.36
1780 2043 1.304713 TTCTACGCCCGGGAGTTCT 60.305 57.895 35.53 13.46 0.00 3.01
1795 2058 1.911766 TTCTTCCGGCTTCTCCCGT 60.912 57.895 0.00 0.00 46.71 5.28
1821 2084 2.202623 GACTGCGGCGAGTACCTG 60.203 66.667 12.98 0.00 0.00 4.00
1848 2111 2.202756 GAGTCCATGGTCGACGCC 60.203 66.667 12.58 0.00 35.33 5.68
1903 2166 0.528470 GACGACAGAGGAGAAGGTGG 59.472 60.000 0.00 0.00 0.00 4.61
2028 2291 3.628646 GACCAGGATGCACCGGCTT 62.629 63.158 0.00 0.00 44.74 4.35
2053 2316 4.547367 GCGTCCAGGGCGGCTTAT 62.547 66.667 17.03 0.00 33.14 1.73
2105 2368 3.056328 GTTGGTCAGGAAGGCGGC 61.056 66.667 0.00 0.00 0.00 6.53
2139 2402 1.959226 GTTGCTGTCCGGCGAGAAA 60.959 57.895 9.30 0.00 34.52 2.52
2221 2484 1.911357 TGGACTCCTGCTTCACATGAT 59.089 47.619 0.00 0.00 0.00 2.45
2274 2537 5.628130 CATGACCTTAGGATCCATCACAAT 58.372 41.667 15.82 0.00 0.00 2.71
2281 2544 9.170890 ACCTTAGGATCCATCACAATATAGAAA 57.829 33.333 15.82 0.00 0.00 2.52
2289 2552 8.279970 TCCATCACAATATAGAAAGTGTTTGG 57.720 34.615 0.00 0.00 37.52 3.28
2305 2593 8.706322 AAGTGTTTGGTATCCTATGAGTTTTT 57.294 30.769 0.00 0.00 0.00 1.94
2336 2624 5.412286 ACATTTCTTTGTGCTTGCAACTTTT 59.588 32.000 0.00 0.00 0.00 2.27
2337 2625 4.925061 TTCTTTGTGCTTGCAACTTTTG 57.075 36.364 0.00 0.00 0.00 2.44
2361 2649 6.601613 TGGAATAAGCCGATTCAAATTAGTGT 59.398 34.615 9.67 0.00 37.53 3.55
2364 2652 3.016736 AGCCGATTCAAATTAGTGTGGG 58.983 45.455 0.00 0.00 0.00 4.61
2369 2657 5.127031 CCGATTCAAATTAGTGTGGGGAATT 59.873 40.000 0.00 0.00 0.00 2.17
2392 2682 5.766150 TTTTTGTCGATCACCAACAGAAT 57.234 34.783 0.00 0.00 0.00 2.40
2436 2728 6.767524 TTTTTAGAACAAAGGCTCAAGTCA 57.232 33.333 0.00 0.00 0.00 3.41
2480 2772 1.202927 CCATCAACCGGCCAGGATTAT 60.203 52.381 18.74 3.23 45.00 1.28
2482 2774 3.497763 CCATCAACCGGCCAGGATTATAA 60.498 47.826 18.74 0.00 45.00 0.98
2502 2795 3.208747 ACAACCACCAACTTACAGAGG 57.791 47.619 0.00 0.00 0.00 3.69
2548 2841 1.953772 CAGAGTGCTGTGCATGCAA 59.046 52.632 24.58 11.95 41.91 4.08
2630 2929 1.519455 GACGATGAAGCCCTCCACG 60.519 63.158 0.00 0.00 0.00 4.94
2723 3022 0.259065 AGCTCCATAGACTCCGACCA 59.741 55.000 0.00 0.00 0.00 4.02
2808 3107 1.651987 ATCCGTCGAACGATGCAAAT 58.348 45.000 10.40 2.31 46.05 2.32
2973 3273 1.303561 GTGGGGCTGCTGATGACAA 60.304 57.895 0.00 0.00 0.00 3.18
2996 3301 0.105760 AACAATGGTGGGAAGCCACA 60.106 50.000 0.00 0.00 41.97 4.17
2997 3302 0.114954 ACAATGGTGGGAAGCCACAT 59.885 50.000 0.00 0.00 41.97 3.21
2998 3303 0.533491 CAATGGTGGGAAGCCACATG 59.467 55.000 0.00 0.00 41.97 3.21
2999 3304 0.409092 AATGGTGGGAAGCCACATGA 59.591 50.000 0.00 0.00 41.97 3.07
3000 3305 0.323725 ATGGTGGGAAGCCACATGAC 60.324 55.000 0.00 0.00 41.97 3.06
3008 3313 2.485814 GGAAGCCACATGACTGAACTTC 59.514 50.000 0.00 5.29 32.93 3.01
3029 3334 1.226746 GGAAGAACCACCAAGACACG 58.773 55.000 0.00 0.00 38.79 4.49
3081 3387 1.056660 ACCAACCAGACCGAACTCAT 58.943 50.000 0.00 0.00 0.00 2.90
3087 3393 1.208052 CCAGACCGAACTCATCACCAT 59.792 52.381 0.00 0.00 0.00 3.55
3091 3397 0.833287 CCGAACTCATCACCATCCCT 59.167 55.000 0.00 0.00 0.00 4.20
3095 3401 0.257039 ACTCATCACCATCCCTTGCC 59.743 55.000 0.00 0.00 0.00 4.52
3098 3405 0.324552 CATCACCATCCCTTGCCCAA 60.325 55.000 0.00 0.00 0.00 4.12
3101 3408 2.755469 CCATCCCTTGCCCAACGG 60.755 66.667 0.00 0.00 0.00 4.44
3135 3442 2.912020 GGGACCCCGACTCATAAGT 58.088 57.895 0.00 0.00 38.88 2.24
3146 3453 3.879427 GACTCATAAGTCGAGATCACCG 58.121 50.000 0.00 0.00 42.42 4.94
3147 3454 3.542648 ACTCATAAGTCGAGATCACCGA 58.457 45.455 6.19 6.19 34.47 4.69
3148 3455 3.945921 ACTCATAAGTCGAGATCACCGAA 59.054 43.478 11.01 0.00 37.81 4.30
3149 3456 4.580995 ACTCATAAGTCGAGATCACCGAAT 59.419 41.667 11.01 7.98 37.81 3.34
3150 3457 4.860072 TCATAAGTCGAGATCACCGAATG 58.140 43.478 11.01 11.19 37.81 2.67
3151 3458 1.927895 AAGTCGAGATCACCGAATGC 58.072 50.000 11.01 1.43 37.81 3.56
3152 3459 0.817654 AGTCGAGATCACCGAATGCA 59.182 50.000 11.01 0.00 37.81 3.96
3153 3460 0.924090 GTCGAGATCACCGAATGCAC 59.076 55.000 11.01 0.00 37.81 4.57
3154 3461 0.525455 TCGAGATCACCGAATGCACG 60.525 55.000 7.61 0.00 32.64 5.34
3155 3462 0.802222 CGAGATCACCGAATGCACGT 60.802 55.000 0.00 0.00 0.00 4.49
3156 3463 0.647410 GAGATCACCGAATGCACGTG 59.353 55.000 12.28 12.28 0.00 4.49
3157 3464 0.037326 AGATCACCGAATGCACGTGT 60.037 50.000 18.38 0.00 0.00 4.49
3158 3465 1.203758 AGATCACCGAATGCACGTGTA 59.796 47.619 18.38 14.09 0.00 2.90
3159 3466 1.323534 GATCACCGAATGCACGTGTAC 59.676 52.381 18.38 1.32 0.00 2.90
3160 3467 0.032267 TCACCGAATGCACGTGTACA 59.968 50.000 18.38 7.94 0.00 2.90
3161 3468 0.438445 CACCGAATGCACGTGTACAG 59.562 55.000 18.38 7.58 0.00 2.74
3162 3469 0.032952 ACCGAATGCACGTGTACAGT 59.967 50.000 18.38 6.62 0.00 3.55
3163 3470 0.438445 CCGAATGCACGTGTACAGTG 59.562 55.000 18.38 16.47 42.15 3.66
3164 3471 1.414378 CGAATGCACGTGTACAGTGA 58.586 50.000 18.38 11.82 41.83 3.41
3165 3472 1.992667 CGAATGCACGTGTACAGTGAT 59.007 47.619 18.38 13.02 41.83 3.06
3166 3473 2.028045 CGAATGCACGTGTACAGTGATC 59.972 50.000 18.38 16.15 41.83 2.92
3167 3474 2.010145 ATGCACGTGTACAGTGATCC 57.990 50.000 18.38 10.21 41.83 3.36
3168 3475 0.037697 TGCACGTGTACAGTGATCCC 60.038 55.000 18.38 9.96 41.83 3.85
3169 3476 0.037697 GCACGTGTACAGTGATCCCA 60.038 55.000 18.38 0.00 41.83 4.37
3170 3477 1.996292 CACGTGTACAGTGATCCCAG 58.004 55.000 7.58 0.00 41.83 4.45
3171 3478 1.544246 CACGTGTACAGTGATCCCAGA 59.456 52.381 7.58 0.00 41.83 3.86
3172 3479 1.819288 ACGTGTACAGTGATCCCAGAG 59.181 52.381 0.00 0.00 0.00 3.35
3173 3480 2.092323 CGTGTACAGTGATCCCAGAGA 58.908 52.381 0.00 0.00 0.00 3.10
3174 3481 2.690497 CGTGTACAGTGATCCCAGAGAT 59.310 50.000 0.00 0.00 38.17 2.75
3184 3491 2.996249 TCCCAGAGATCAATGCTCAC 57.004 50.000 0.00 0.00 34.85 3.51
3185 3492 2.475155 TCCCAGAGATCAATGCTCACT 58.525 47.619 0.00 0.00 34.85 3.41
3186 3493 2.169978 TCCCAGAGATCAATGCTCACTG 59.830 50.000 4.87 4.87 34.85 3.66
3187 3494 2.169978 CCCAGAGATCAATGCTCACTGA 59.830 50.000 11.95 0.00 34.46 3.41
3188 3495 3.370209 CCCAGAGATCAATGCTCACTGAA 60.370 47.826 11.95 0.00 34.46 3.02
3189 3496 3.622163 CCAGAGATCAATGCTCACTGAAC 59.378 47.826 11.95 0.00 34.46 3.18
3190 3497 4.251268 CAGAGATCAATGCTCACTGAACA 58.749 43.478 5.78 0.00 34.46 3.18
3191 3498 4.093115 CAGAGATCAATGCTCACTGAACAC 59.907 45.833 5.78 0.00 34.46 3.32
3192 3499 3.999001 GAGATCAATGCTCACTGAACACA 59.001 43.478 0.00 0.00 32.67 3.72
3193 3500 3.750130 AGATCAATGCTCACTGAACACAC 59.250 43.478 0.00 0.00 0.00 3.82
3194 3501 2.916640 TCAATGCTCACTGAACACACA 58.083 42.857 0.00 0.00 0.00 3.72
3195 3502 2.874086 TCAATGCTCACTGAACACACAG 59.126 45.455 0.00 0.00 42.78 3.66
3196 3503 2.874086 CAATGCTCACTGAACACACAGA 59.126 45.455 0.00 0.00 40.63 3.41
3197 3504 2.689553 TGCTCACTGAACACACAGAA 57.310 45.000 0.00 0.00 40.63 3.02
3198 3505 2.984562 TGCTCACTGAACACACAGAAA 58.015 42.857 0.00 0.00 40.63 2.52
3199 3506 2.677836 TGCTCACTGAACACACAGAAAC 59.322 45.455 0.00 0.00 40.63 2.78
3200 3507 2.939103 GCTCACTGAACACACAGAAACT 59.061 45.455 0.00 0.00 40.63 2.66
3201 3508 3.242543 GCTCACTGAACACACAGAAACTG 60.243 47.826 0.00 0.00 40.63 3.16
3202 3509 4.183865 CTCACTGAACACACAGAAACTGA 58.816 43.478 5.76 0.00 40.63 3.41
3203 3510 4.574892 TCACTGAACACACAGAAACTGAA 58.425 39.130 5.76 0.00 40.63 3.02
3204 3511 5.185454 TCACTGAACACACAGAAACTGAAT 58.815 37.500 5.76 0.00 40.63 2.57
3205 3512 6.345298 TCACTGAACACACAGAAACTGAATA 58.655 36.000 5.76 0.00 40.63 1.75
3206 3513 6.821160 TCACTGAACACACAGAAACTGAATAA 59.179 34.615 5.76 0.00 40.63 1.40
3207 3514 6.907212 CACTGAACACACAGAAACTGAATAAC 59.093 38.462 5.76 0.00 40.63 1.89
3208 3515 6.597672 ACTGAACACACAGAAACTGAATAACA 59.402 34.615 5.76 0.00 40.63 2.41
3209 3516 7.120579 ACTGAACACACAGAAACTGAATAACAA 59.879 33.333 5.76 0.00 40.63 2.83
3210 3517 7.471721 TGAACACACAGAAACTGAATAACAAG 58.528 34.615 5.76 0.00 35.18 3.16
3211 3518 7.335673 TGAACACACAGAAACTGAATAACAAGA 59.664 33.333 5.76 0.00 35.18 3.02
3212 3519 7.251704 ACACACAGAAACTGAATAACAAGAG 57.748 36.000 5.76 0.00 35.18 2.85
3213 3520 6.823689 ACACACAGAAACTGAATAACAAGAGT 59.176 34.615 5.76 0.00 35.18 3.24
3214 3521 7.011482 ACACACAGAAACTGAATAACAAGAGTC 59.989 37.037 5.76 0.00 35.18 3.36
3215 3522 7.225538 CACACAGAAACTGAATAACAAGAGTCT 59.774 37.037 5.76 0.00 35.18 3.24
3216 3523 7.770897 ACACAGAAACTGAATAACAAGAGTCTT 59.229 33.333 0.00 0.00 35.18 3.01
3217 3524 9.261180 CACAGAAACTGAATAACAAGAGTCTTA 57.739 33.333 4.74 0.00 35.18 2.10
3218 3525 9.262358 ACAGAAACTGAATAACAAGAGTCTTAC 57.738 33.333 4.74 0.00 35.18 2.34
3219 3526 9.261180 CAGAAACTGAATAACAAGAGTCTTACA 57.739 33.333 4.74 0.00 32.44 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 77 1.508632 CGTGCCTCTTTCGAAAAGGA 58.491 50.000 28.33 17.09 31.44 3.36
78 83 4.735132 CGGGCGTGCCTCTTTCGA 62.735 66.667 11.25 0.00 36.10 3.71
106 111 5.183140 CCGAAAGAGGTATGGTTGTGATTTT 59.817 40.000 0.00 0.00 0.00 1.82
118 123 3.756963 GGTTTTGCTTCCGAAAGAGGTAT 59.243 43.478 0.00 0.00 34.14 2.73
120 125 1.954382 GGTTTTGCTTCCGAAAGAGGT 59.046 47.619 0.00 0.00 34.14 3.85
130 135 1.192534 CGAGAGTCACGGTTTTGCTTC 59.807 52.381 1.62 0.00 0.00 3.86
141 146 0.038526 TTTCCTTCCGCGAGAGTCAC 60.039 55.000 8.23 0.00 0.00 3.67
185 190 1.595929 GGTCGTGCCTTGGAAACGA 60.596 57.895 11.99 11.99 43.50 3.85
193 198 0.247736 GAGAGTCATGGTCGTGCCTT 59.752 55.000 0.00 0.00 38.35 4.35
196 201 0.524392 CTCGAGAGTCATGGTCGTGC 60.524 60.000 6.58 0.00 35.22 5.34
197 202 1.087501 TCTCGAGAGTCATGGTCGTG 58.912 55.000 12.08 0.00 35.22 4.35
198 203 1.822506 TTCTCGAGAGTCATGGTCGT 58.177 50.000 15.94 0.00 35.22 4.34
199 204 2.791567 CTTTCTCGAGAGTCATGGTCG 58.208 52.381 15.94 0.00 34.98 4.79
200 205 2.094494 TGCTTTCTCGAGAGTCATGGTC 60.094 50.000 15.94 1.59 0.00 4.02
201 206 1.895798 TGCTTTCTCGAGAGTCATGGT 59.104 47.619 15.94 0.00 0.00 3.55
202 207 2.266554 GTGCTTTCTCGAGAGTCATGG 58.733 52.381 15.94 4.89 0.00 3.66
203 208 2.951726 TGTGCTTTCTCGAGAGTCATG 58.048 47.619 15.94 4.78 0.00 3.07
204 209 3.321497 GTTGTGCTTTCTCGAGAGTCAT 58.679 45.455 15.94 0.00 0.00 3.06
205 210 2.545952 GGTTGTGCTTTCTCGAGAGTCA 60.546 50.000 15.94 11.63 0.00 3.41
206 211 2.062519 GGTTGTGCTTTCTCGAGAGTC 58.937 52.381 15.94 9.19 0.00 3.36
207 212 1.603172 CGGTTGTGCTTTCTCGAGAGT 60.603 52.381 15.94 0.00 0.00 3.24
208 213 1.063806 CGGTTGTGCTTTCTCGAGAG 58.936 55.000 15.94 6.26 0.00 3.20
209 214 0.387929 ACGGTTGTGCTTTCTCGAGA 59.612 50.000 12.08 12.08 0.00 4.04
210 215 0.508641 CACGGTTGTGCTTTCTCGAG 59.491 55.000 5.93 5.93 39.67 4.04
211 216 2.600388 CACGGTTGTGCTTTCTCGA 58.400 52.632 0.00 0.00 39.67 4.04
230 235 1.497722 GTTTTGCTTCCGCGAGAGG 59.502 57.895 8.23 4.88 39.65 3.69
231 236 1.227999 TGGTTTTGCTTCCGCGAGAG 61.228 55.000 8.23 5.93 39.65 3.20
232 237 0.605319 ATGGTTTTGCTTCCGCGAGA 60.605 50.000 8.23 0.00 39.65 4.04
233 238 0.454957 CATGGTTTTGCTTCCGCGAG 60.455 55.000 8.23 0.00 39.65 5.03
234 239 0.886938 TCATGGTTTTGCTTCCGCGA 60.887 50.000 8.23 0.00 39.65 5.87
235 240 0.729140 GTCATGGTTTTGCTTCCGCG 60.729 55.000 0.00 0.00 39.65 6.46
236 241 0.598065 AGTCATGGTTTTGCTTCCGC 59.402 50.000 0.00 0.00 0.00 5.54
237 242 2.154462 AGAGTCATGGTTTTGCTTCCG 58.846 47.619 0.00 0.00 0.00 4.30
238 243 2.160417 CGAGAGTCATGGTTTTGCTTCC 59.840 50.000 0.00 0.00 0.00 3.46
239 244 2.808543 ACGAGAGTCATGGTTTTGCTTC 59.191 45.455 0.00 0.00 44.19 3.86
240 245 2.851195 ACGAGAGTCATGGTTTTGCTT 58.149 42.857 0.00 0.00 44.19 3.91
241 246 2.550830 ACGAGAGTCATGGTTTTGCT 57.449 45.000 0.00 0.00 44.19 3.91
290 295 2.223386 CGTGCCTCTTGGAAACGAAAAA 60.223 45.455 0.00 0.00 43.27 1.94
291 296 1.332375 CGTGCCTCTTGGAAACGAAAA 59.668 47.619 0.00 0.00 43.27 2.29
292 297 0.941542 CGTGCCTCTTGGAAACGAAA 59.058 50.000 0.00 0.00 43.27 3.46
293 298 0.105224 TCGTGCCTCTTGGAAACGAA 59.895 50.000 9.76 0.00 44.88 3.85
294 299 0.599204 GTCGTGCCTCTTGGAAACGA 60.599 55.000 8.59 8.59 45.30 3.85
295 300 0.878523 TGTCGTGCCTCTTGGAAACG 60.879 55.000 0.00 0.00 42.52 3.60
296 301 0.868406 CTGTCGTGCCTCTTGGAAAC 59.132 55.000 0.00 0.00 34.57 2.78
297 302 0.468226 ACTGTCGTGCCTCTTGGAAA 59.532 50.000 0.00 0.00 34.57 3.13
298 303 0.249868 CACTGTCGTGCCTCTTGGAA 60.250 55.000 0.00 0.00 33.82 3.53
299 304 1.112916 TCACTGTCGTGCCTCTTGGA 61.113 55.000 0.00 0.00 40.99 3.53
300 305 0.946221 GTCACTGTCGTGCCTCTTGG 60.946 60.000 0.00 0.00 40.99 3.61
301 306 0.032678 AGTCACTGTCGTGCCTCTTG 59.967 55.000 0.00 0.00 40.99 3.02
302 307 0.315568 GAGTCACTGTCGTGCCTCTT 59.684 55.000 0.00 0.00 41.61 2.85
303 308 1.528292 GGAGTCACTGTCGTGCCTCT 61.528 60.000 3.93 0.00 43.68 3.69
304 309 1.080434 GGAGTCACTGTCGTGCCTC 60.080 63.158 0.00 0.00 43.52 4.70
305 310 1.531840 AGGAGTCACTGTCGTGCCT 60.532 57.895 0.00 0.00 40.99 4.75
306 311 1.373497 CAGGAGTCACTGTCGTGCC 60.373 63.158 0.00 0.00 40.99 5.01
307 312 4.251760 CAGGAGTCACTGTCGTGC 57.748 61.111 0.00 0.00 40.99 5.34
313 318 2.625314 TCAAGAGTCACAGGAGTCACTG 59.375 50.000 6.98 6.98 44.45 3.66
314 319 2.950781 TCAAGAGTCACAGGAGTCACT 58.049 47.619 0.00 0.00 44.45 3.41
315 320 3.951775 ATCAAGAGTCACAGGAGTCAC 57.048 47.619 0.00 0.00 44.45 3.67
316 321 4.963318 AAATCAAGAGTCACAGGAGTCA 57.037 40.909 0.00 0.00 44.45 3.41
362 367 1.272872 ACAGCCATGCCTCTTGGAAAT 60.273 47.619 3.29 0.00 36.26 2.17
368 373 0.035630 GAGTCACAGCCATGCCTCTT 60.036 55.000 0.00 0.00 0.00 2.85
376 381 2.082629 TTTCGCGAGAGTCACAGCCA 62.083 55.000 9.59 0.00 43.69 4.75
380 385 1.605232 TGTACTTTCGCGAGAGTCACA 59.395 47.619 32.47 27.52 43.69 3.58
397 402 2.345991 GCGGGAGGCACAGTTGTA 59.654 61.111 0.00 0.00 42.87 2.41
483 683 4.039357 CGAGAGTCACGGCCGTGT 62.039 66.667 46.56 34.60 45.55 4.49
503 726 7.931407 ACAAAGTGTTTTCAGTTCTTTTCCTTT 59.069 29.630 0.00 0.00 41.95 3.11
504 727 7.441836 ACAAAGTGTTTTCAGTTCTTTTCCTT 58.558 30.769 0.00 0.00 41.95 3.36
505 728 6.993079 ACAAAGTGTTTTCAGTTCTTTTCCT 58.007 32.000 0.00 0.00 41.95 3.36
506 729 7.652300 AACAAAGTGTTTTCAGTTCTTTTCC 57.348 32.000 0.00 0.00 41.95 3.13
541 764 1.878522 GTCACAGCCGTGCCTATCG 60.879 63.158 0.00 0.00 43.28 2.92
542 765 0.528684 GAGTCACAGCCGTGCCTATC 60.529 60.000 0.00 0.00 43.28 2.08
543 766 0.972983 AGAGTCACAGCCGTGCCTAT 60.973 55.000 0.00 0.00 43.28 2.57
544 767 1.595993 GAGAGTCACAGCCGTGCCTA 61.596 60.000 0.00 0.00 43.28 3.93
545 768 2.919856 AGAGTCACAGCCGTGCCT 60.920 61.111 0.00 0.00 43.28 4.75
546 769 2.433318 GAGAGTCACAGCCGTGCC 60.433 66.667 0.00 0.00 43.28 5.01
547 770 2.807045 CGAGAGTCACAGCCGTGC 60.807 66.667 0.00 0.00 43.28 5.34
548 771 2.807045 GCGAGAGTCACAGCCGTG 60.807 66.667 0.00 0.00 45.08 4.94
549 772 2.363711 TTTGCGAGAGTCACAGCCGT 62.364 55.000 0.00 0.00 0.00 5.68
550 773 1.221466 TTTTGCGAGAGTCACAGCCG 61.221 55.000 0.00 0.00 0.00 5.52
551 774 0.514691 CTTTTGCGAGAGTCACAGCC 59.485 55.000 0.00 0.00 0.00 4.85
552 775 0.110464 GCTTTTGCGAGAGTCACAGC 60.110 55.000 0.00 0.00 34.86 4.40
565 788 3.420839 AGAGTCACGGTTTTGCTTTTG 57.579 42.857 0.00 0.00 0.00 2.44
566 789 3.769536 CAAGAGTCACGGTTTTGCTTTT 58.230 40.909 0.00 0.00 0.00 2.27
660 901 3.560668 GGTTTTCCACCGGTCTTCCTTAT 60.561 47.826 2.59 0.00 40.31 1.73
689 930 4.394439 TTGGCTTTTTAGCGGTTTTTCT 57.606 36.364 0.00 0.00 35.24 2.52
690 931 5.472320 TTTTGGCTTTTTAGCGGTTTTTC 57.528 34.783 0.00 0.00 35.24 2.29
696 937 2.159854 CGCATTTTTGGCTTTTTAGCGG 60.160 45.455 0.00 0.00 39.07 5.52
697 938 2.474735 ACGCATTTTTGGCTTTTTAGCG 59.525 40.909 0.00 0.00 46.98 4.26
698 939 3.247411 ACACGCATTTTTGGCTTTTTAGC 59.753 39.130 0.00 0.00 0.00 3.09
700 941 3.557595 CCACACGCATTTTTGGCTTTTTA 59.442 39.130 0.00 0.00 0.00 1.52
733 977 2.814336 GACGCTCCCTTCAGATTTTGTT 59.186 45.455 0.00 0.00 0.00 2.83
734 978 2.427506 GACGCTCCCTTCAGATTTTGT 58.572 47.619 0.00 0.00 0.00 2.83
735 979 1.394917 CGACGCTCCCTTCAGATTTTG 59.605 52.381 0.00 0.00 0.00 2.44
742 986 2.701780 GCTCTCGACGCTCCCTTCA 61.702 63.158 0.00 0.00 0.00 3.02
788 1032 3.317150 CAACTATCAGCGTCACTTGACA 58.683 45.455 9.94 0.00 44.99 3.58
818 1062 1.267806 AGTTAACGAGCGTTCCTTCGA 59.732 47.619 11.89 0.00 39.31 3.71
826 1070 2.228343 AGAGCAACTAGTTAACGAGCGT 59.772 45.455 14.82 1.65 0.00 5.07
864 1108 3.719871 TGCAAGTAACAGAGATCCCCTA 58.280 45.455 0.00 0.00 0.00 3.53
865 1109 2.551270 TGCAAGTAACAGAGATCCCCT 58.449 47.619 0.00 0.00 0.00 4.79
866 1110 3.567478 ATGCAAGTAACAGAGATCCCC 57.433 47.619 0.00 0.00 0.00 4.81
886 1130 4.284234 GCCCACTTATATTAGGGTTCCGTA 59.716 45.833 0.00 0.00 43.42 4.02
890 1134 6.214819 TCCATAGCCCACTTATATTAGGGTTC 59.785 42.308 0.00 0.00 43.42 3.62
913 1157 2.327325 TATAGGTGAGATGGGCCTCC 57.673 55.000 4.53 0.00 34.07 4.30
929 1179 7.684317 TCTCAACCCTTGGTCATGTTATATA 57.316 36.000 0.00 0.00 33.12 0.86
930 1180 6.575244 TCTCAACCCTTGGTCATGTTATAT 57.425 37.500 0.00 0.00 33.12 0.86
967 1217 1.139058 GCCGTGGTGTAGAGATTGGAT 59.861 52.381 0.00 0.00 0.00 3.41
1216 1473 1.609635 TAGCCGGCGAGTGGATGAAA 61.610 55.000 23.20 0.00 0.00 2.69
1233 1490 0.459237 GGCCAGATCGATCGGCATAG 60.459 60.000 37.83 21.62 43.41 2.23
1238 1495 2.256764 CTCGGCCAGATCGATCGG 59.743 66.667 23.49 23.49 36.01 4.18
1250 1507 1.878953 TCAAAAACTCAGGACTCGGC 58.121 50.000 0.00 0.00 0.00 5.54
1261 1518 1.147817 ACCTGCAGGGGATCAAAAACT 59.852 47.619 35.42 8.04 40.27 2.66
1267 1524 4.100084 CGCACCTGCAGGGGATCA 62.100 66.667 39.55 0.00 42.67 2.92
1449 1709 0.977627 AGGATCATGAGGACGGCACA 60.978 55.000 0.09 0.00 0.00 4.57
1709 1972 2.093341 AGGACTTGTTGGTACACGTTGT 60.093 45.455 0.00 0.00 39.29 3.32
1713 1976 3.504906 TCTCTAGGACTTGTTGGTACACG 59.495 47.826 0.00 0.00 39.29 4.49
1723 1986 2.482142 GGAACGGCATCTCTAGGACTTG 60.482 54.545 0.00 0.00 0.00 3.16
1726 1989 1.338655 GAGGAACGGCATCTCTAGGAC 59.661 57.143 0.00 0.00 0.00 3.85
1731 1994 1.810532 GTCGAGGAACGGCATCTCT 59.189 57.895 0.00 0.00 46.56 3.10
1780 2043 3.755628 CGACGGGAGAAGCCGGAA 61.756 66.667 5.05 0.00 40.07 4.30
1818 2081 0.318441 TGGACTCGACTTTGCTCAGG 59.682 55.000 0.00 0.00 0.00 3.86
1821 2084 1.338200 ACCATGGACTCGACTTTGCTC 60.338 52.381 21.47 0.00 0.00 4.26
2053 2316 4.429212 CACGTCCGTCATGGCCGA 62.429 66.667 0.00 0.00 37.80 5.54
2058 2321 0.528466 CCTCCATCACGTCCGTCATG 60.528 60.000 0.00 0.00 0.00 3.07
2063 2326 2.105128 GAGCCTCCATCACGTCCG 59.895 66.667 0.00 0.00 0.00 4.79
2139 2402 3.255395 CGATCATCTCAGCATACCTGTCT 59.745 47.826 0.00 0.00 42.38 3.41
2240 2503 0.324943 AAGGTCATGCGTGGCTACTT 59.675 50.000 10.92 3.31 0.00 2.24
2251 2514 4.694760 TGTGATGGATCCTAAGGTCATG 57.305 45.455 14.23 0.00 0.00 3.07
2281 2544 7.942341 TCAAAAACTCATAGGATACCAAACACT 59.058 33.333 0.00 0.00 37.17 3.55
2289 2552 8.948631 TGTGATCTCAAAAACTCATAGGATAC 57.051 34.615 0.00 0.00 0.00 2.24
2336 2624 6.601613 ACACTAATTTGAATCGGCTTATTCCA 59.398 34.615 8.47 0.00 35.40 3.53
2337 2625 6.912591 CACACTAATTTGAATCGGCTTATTCC 59.087 38.462 8.47 0.00 35.40 3.01
2375 2663 4.929808 ACACTTATTCTGTTGGTGATCGAC 59.070 41.667 0.00 0.00 0.00 4.20
2380 2670 7.581213 AAATTCACACTTATTCTGTTGGTGA 57.419 32.000 0.00 0.00 32.52 4.02
2448 2740 4.565022 CCGGTTGATGGCTTTGTTAATTT 58.435 39.130 0.00 0.00 0.00 1.82
2480 2772 4.710324 CCTCTGTAAGTTGGTGGTTGTTA 58.290 43.478 0.00 0.00 33.76 2.41
2482 2774 2.748465 GCCTCTGTAAGTTGGTGGTTGT 60.748 50.000 0.00 0.00 32.83 3.32
2502 2795 5.942325 TTTTAGCTGTTTCTTTGTTTCGC 57.058 34.783 0.00 0.00 0.00 4.70
2544 2837 3.778075 TGGTAGGAAGCCTATTAGTTGCA 59.222 43.478 0.00 0.00 38.48 4.08
2548 2841 6.621394 TGTAGATGGTAGGAAGCCTATTAGT 58.379 40.000 0.00 0.00 38.48 2.24
2630 2929 3.443045 CAGGGTGGATTGCACGCC 61.443 66.667 19.32 13.09 36.34 5.68
2723 3022 4.345859 TGTAGGAGGTTGTCAACGATTT 57.654 40.909 9.57 0.00 0.00 2.17
2788 3087 1.434555 TTTGCATCGTTCGACGGATT 58.565 45.000 0.00 0.00 42.81 3.01
2933 3232 2.287788 CGTGCATTTTGCTTCTCCTTGT 60.288 45.455 0.00 0.00 45.31 3.16
2973 3273 0.681175 GCTTCCCACCATTGTTGCTT 59.319 50.000 0.00 0.00 0.00 3.91
2996 3301 3.557264 GGTTCTTCCCGAAGTTCAGTCAT 60.557 47.826 3.32 0.00 39.38 3.06
2997 3302 2.224209 GGTTCTTCCCGAAGTTCAGTCA 60.224 50.000 3.32 0.00 39.38 3.41
2998 3303 2.224209 TGGTTCTTCCCGAAGTTCAGTC 60.224 50.000 3.32 0.00 39.38 3.51
2999 3304 1.766496 TGGTTCTTCCCGAAGTTCAGT 59.234 47.619 3.32 0.00 39.38 3.41
3000 3305 2.143925 GTGGTTCTTCCCGAAGTTCAG 58.856 52.381 3.32 0.00 39.38 3.02
3008 3313 0.107831 TGTCTTGGTGGTTCTTCCCG 59.892 55.000 0.00 0.00 34.77 5.14
3029 3334 1.880027 GTGACATGGTTGGAGTTGGTC 59.120 52.381 0.00 0.00 0.00 4.02
3081 3387 1.076549 GTTGGGCAAGGGATGGTGA 59.923 57.895 0.00 0.00 0.00 4.02
3113 3420 2.170908 TATGAGTCGGGGTCCCCACA 62.171 60.000 27.45 19.30 45.83 4.17
3114 3421 0.979187 TTATGAGTCGGGGTCCCCAC 60.979 60.000 27.45 21.74 45.83 4.61
3115 3422 0.689745 CTTATGAGTCGGGGTCCCCA 60.690 60.000 27.45 11.28 45.83 4.96
3116 3423 0.690077 ACTTATGAGTCGGGGTCCCC 60.690 60.000 18.34 18.34 41.09 4.81
3117 3424 0.751452 GACTTATGAGTCGGGGTCCC 59.249 60.000 0.00 0.00 42.60 4.46
3126 3433 3.542648 TCGGTGATCTCGACTTATGAGT 58.457 45.455 7.46 0.00 39.32 3.41
3127 3434 4.553756 TTCGGTGATCTCGACTTATGAG 57.446 45.455 10.38 0.00 36.30 2.90
3128 3435 4.793028 GCATTCGGTGATCTCGACTTATGA 60.793 45.833 17.77 4.78 36.30 2.15
3129 3436 3.426859 GCATTCGGTGATCTCGACTTATG 59.573 47.826 10.38 11.96 36.30 1.90
3130 3437 3.068165 TGCATTCGGTGATCTCGACTTAT 59.932 43.478 10.38 1.55 36.30 1.73
3131 3438 2.425668 TGCATTCGGTGATCTCGACTTA 59.574 45.455 10.38 0.00 36.30 2.24
3132 3439 1.204704 TGCATTCGGTGATCTCGACTT 59.795 47.619 10.38 1.19 36.30 3.01
3133 3440 0.817654 TGCATTCGGTGATCTCGACT 59.182 50.000 10.38 4.24 36.30 4.18
3134 3441 0.924090 GTGCATTCGGTGATCTCGAC 59.076 55.000 10.38 2.52 36.30 4.20
3135 3442 0.525455 CGTGCATTCGGTGATCTCGA 60.525 55.000 7.46 7.46 34.62 4.04
3136 3443 0.802222 ACGTGCATTCGGTGATCTCG 60.802 55.000 1.59 0.00 34.94 4.04
3137 3444 0.647410 CACGTGCATTCGGTGATCTC 59.353 55.000 0.82 0.00 34.94 2.75
3138 3445 0.037326 ACACGTGCATTCGGTGATCT 60.037 50.000 17.22 0.00 34.94 2.75
3139 3446 1.323534 GTACACGTGCATTCGGTGATC 59.676 52.381 17.22 0.00 34.94 2.92
3140 3447 1.337354 TGTACACGTGCATTCGGTGAT 60.337 47.619 17.22 0.00 34.94 3.06
3141 3448 0.032267 TGTACACGTGCATTCGGTGA 59.968 50.000 17.22 0.00 34.94 4.02
3142 3449 0.438445 CTGTACACGTGCATTCGGTG 59.562 55.000 17.22 5.33 34.94 4.94
3143 3450 0.032952 ACTGTACACGTGCATTCGGT 59.967 50.000 17.22 11.47 34.94 4.69
3144 3451 0.438445 CACTGTACACGTGCATTCGG 59.562 55.000 17.22 10.84 34.94 4.30
3145 3452 1.414378 TCACTGTACACGTGCATTCG 58.586 50.000 17.22 3.13 32.54 3.34
3146 3453 2.348666 GGATCACTGTACACGTGCATTC 59.651 50.000 17.22 4.22 32.54 2.67
3147 3454 2.346803 GGATCACTGTACACGTGCATT 58.653 47.619 17.22 0.00 32.54 3.56
3148 3455 1.405526 GGGATCACTGTACACGTGCAT 60.406 52.381 17.22 0.00 32.54 3.96
3149 3456 0.037697 GGGATCACTGTACACGTGCA 60.038 55.000 17.22 5.50 32.54 4.57
3150 3457 0.037697 TGGGATCACTGTACACGTGC 60.038 55.000 17.22 0.00 32.54 5.34
3151 3458 1.544246 TCTGGGATCACTGTACACGTG 59.456 52.381 15.48 15.48 0.00 4.49
3152 3459 1.819288 CTCTGGGATCACTGTACACGT 59.181 52.381 0.00 0.00 0.00 4.49
3153 3460 2.092323 TCTCTGGGATCACTGTACACG 58.908 52.381 0.00 0.00 0.00 4.49
3164 3471 3.047115 AGTGAGCATTGATCTCTGGGAT 58.953 45.455 5.75 0.00 37.37 3.85
3165 3472 2.169978 CAGTGAGCATTGATCTCTGGGA 59.830 50.000 20.68 0.00 36.39 4.37
3166 3473 2.169978 TCAGTGAGCATTGATCTCTGGG 59.830 50.000 25.26 8.81 39.18 4.45
3167 3474 3.538634 TCAGTGAGCATTGATCTCTGG 57.461 47.619 25.26 12.68 39.18 3.86
3168 3475 4.093115 GTGTTCAGTGAGCATTGATCTCTG 59.907 45.833 21.84 21.84 39.77 3.35
3169 3476 4.252073 GTGTTCAGTGAGCATTGATCTCT 58.748 43.478 13.12 2.01 0.00 3.10
3170 3477 3.999001 TGTGTTCAGTGAGCATTGATCTC 59.001 43.478 13.12 0.00 0.00 2.75
3171 3478 3.750130 GTGTGTTCAGTGAGCATTGATCT 59.250 43.478 13.12 0.00 0.00 2.75
3172 3479 3.499537 TGTGTGTTCAGTGAGCATTGATC 59.500 43.478 13.12 0.51 0.00 2.92
3173 3480 3.479489 TGTGTGTTCAGTGAGCATTGAT 58.521 40.909 13.12 0.00 0.00 2.57
3174 3481 2.874086 CTGTGTGTTCAGTGAGCATTGA 59.126 45.455 13.12 0.00 0.00 2.57
3175 3482 2.874086 TCTGTGTGTTCAGTGAGCATTG 59.126 45.455 13.12 4.46 36.85 2.82
3176 3483 3.198409 TCTGTGTGTTCAGTGAGCATT 57.802 42.857 13.12 0.00 36.85 3.56
3177 3484 2.916702 TCTGTGTGTTCAGTGAGCAT 57.083 45.000 13.12 0.00 36.85 3.79
3178 3485 2.677836 GTTTCTGTGTGTTCAGTGAGCA 59.322 45.455 5.45 5.45 36.85 4.26
3179 3486 2.939103 AGTTTCTGTGTGTTCAGTGAGC 59.061 45.455 0.00 0.00 36.85 4.26
3180 3487 4.183865 TCAGTTTCTGTGTGTTCAGTGAG 58.816 43.478 0.00 0.00 36.85 3.51
3181 3488 4.200838 TCAGTTTCTGTGTGTTCAGTGA 57.799 40.909 0.00 0.00 36.85 3.41
3182 3489 4.944962 TTCAGTTTCTGTGTGTTCAGTG 57.055 40.909 0.00 0.00 36.85 3.66
3183 3490 6.597672 TGTTATTCAGTTTCTGTGTGTTCAGT 59.402 34.615 0.00 0.00 36.85 3.41
3184 3491 7.015226 TGTTATTCAGTTTCTGTGTGTTCAG 57.985 36.000 0.00 0.00 36.85 3.02
3185 3492 6.993786 TGTTATTCAGTTTCTGTGTGTTCA 57.006 33.333 0.00 0.00 32.61 3.18
3186 3493 7.693952 TCTTGTTATTCAGTTTCTGTGTGTTC 58.306 34.615 0.00 0.00 32.61 3.18
3187 3494 7.336931 ACTCTTGTTATTCAGTTTCTGTGTGTT 59.663 33.333 0.00 0.00 32.61 3.32
3188 3495 6.823689 ACTCTTGTTATTCAGTTTCTGTGTGT 59.176 34.615 0.00 0.00 32.61 3.72
3189 3496 7.225538 AGACTCTTGTTATTCAGTTTCTGTGTG 59.774 37.037 0.00 0.00 32.61 3.82
3190 3497 7.275920 AGACTCTTGTTATTCAGTTTCTGTGT 58.724 34.615 0.00 0.00 32.61 3.72
3191 3498 7.721286 AGACTCTTGTTATTCAGTTTCTGTG 57.279 36.000 0.00 0.00 32.61 3.66
3192 3499 9.262358 GTAAGACTCTTGTTATTCAGTTTCTGT 57.738 33.333 1.17 0.00 32.61 3.41
3193 3500 9.261180 TGTAAGACTCTTGTTATTCAGTTTCTG 57.739 33.333 1.17 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.