Multiple sequence alignment - TraesCS7A01G457100

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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 TraesCS7A01G457100 chr7A 100.000 7051 0 0 1 7051 652696231 652689181 0.000000e+00 13021.0
1 TraesCS7A01G457100 chr7A 99.383 162 1 0 6310 6471 652689841 652689680 1.920000e-75 294.0
2 TraesCS7A01G457100 chr7A 99.383 162 1 0 6391 6552 652689922 652689761 1.920000e-75 294.0
3 TraesCS7A01G457100 chr7A 98.113 106 1 1 2633 2737 652693496 652693391 4.340000e-42 183.0
4 TraesCS7A01G457100 chr7A 98.113 106 1 1 2736 2841 652693599 652693495 4.340000e-42 183.0
5 TraesCS7A01G457100 chr7A 98.765 81 1 0 6310 6390 652689760 652689680 2.050000e-30 145.0
6 TraesCS7A01G457100 chr7A 98.765 81 1 0 6472 6552 652689922 652689842 2.050000e-30 145.0
7 TraesCS7A01G457100 chr7D 94.253 3480 135 27 2949 6391 566455348 566451897 0.000000e+00 5258.0
8 TraesCS7A01G457100 chr7D 95.748 1764 50 11 977 2737 566462570 566460829 0.000000e+00 2819.0
9 TraesCS7A01G457100 chr7D 90.602 415 27 4 366 780 566465506 566465104 2.240000e-149 540.0
10 TraesCS7A01G457100 chr7D 88.783 419 18 6 6632 7027 566450784 566450372 2.960000e-133 486.0
11 TraesCS7A01G457100 chr7D 93.578 218 10 1 2736 2953 566460930 566460717 8.820000e-84 322.0
12 TraesCS7A01G457100 chr7D 85.484 310 21 11 4 313 566465791 566465506 1.150000e-77 302.0
13 TraesCS7A01G457100 chr7D 95.000 160 8 0 6475 6634 566451975 566451816 1.170000e-62 252.0
14 TraesCS7A01G457100 chr7D 82.390 318 12 17 689 982 566463360 566463063 3.290000e-58 237.0
15 TraesCS7A01G457100 chr7D 97.468 79 2 0 6394 6472 566451975 566451897 1.230000e-27 135.0
16 TraesCS7A01G457100 chr7D 100.000 45 0 0 326 370 40483583 40483627 4.530000e-12 84.2
17 TraesCS7A01G457100 chr7D 82.759 87 12 2 6877 6962 73373580 73373496 2.730000e-09 75.0
18 TraesCS7A01G457100 chr7B 92.483 3685 191 48 2736 6390 620757624 620761252 0.000000e+00 5192.0
19 TraesCS7A01G457100 chr7B 95.036 1793 59 11 948 2737 620755960 620757725 0.000000e+00 2791.0
20 TraesCS7A01G457100 chr7B 90.671 343 21 4 4795 5136 619111219 619110887 5.020000e-121 446.0
21 TraesCS7A01G457100 chr7B 87.582 306 27 4 366 671 620706754 620707048 1.880000e-90 344.0
22 TraesCS7A01G457100 chr7B 91.870 123 10 0 191 313 620706632 620706754 9.400000e-39 172.0
23 TraesCS7A01G457100 chr7B 82.635 167 17 9 669 826 620739437 620739600 3.430000e-28 137.0
24 TraesCS7A01G457100 chr7B 95.122 82 4 0 689 770 620755473 620755554 5.740000e-26 130.0
25 TraesCS7A01G457100 chr7B 97.872 47 1 0 326 372 100960605 100960559 1.630000e-11 82.4
26 TraesCS7A01G457100 chr5D 97.778 45 1 0 326 370 51699347 51699303 2.110000e-10 78.7
27 TraesCS7A01G457100 chr4B 97.778 45 1 0 326 370 221000737 221000693 2.110000e-10 78.7
28 TraesCS7A01G457100 chr4A 97.778 45 1 0 326 370 615525464 615525508 2.110000e-10 78.7
29 TraesCS7A01G457100 chr1D 97.778 45 1 0 326 370 50709003 50708959 2.110000e-10 78.7
30 TraesCS7A01G457100 chr1B 91.379 58 4 1 326 383 479429979 479429923 2.110000e-10 78.7
31 TraesCS7A01G457100 chr1B 97.778 45 1 0 324 368 502640989 502640945 2.110000e-10 78.7
32 TraesCS7A01G457100 chr1B 100.000 42 0 0 326 367 643032813 643032854 2.110000e-10 78.7


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 TraesCS7A01G457100 chr7A 652689181 652696231 7050 True 13021.000000 13021 100.000000 1 7051 1 chr7A.!!$R1 7050
1 TraesCS7A01G457100 chr7A 652689680 652693599 3919 True 207.333333 294 98.753667 2633 6552 6 chr7A.!!$R2 3919
2 TraesCS7A01G457100 chr7D 566450372 566455348 4976 True 1532.750000 5258 93.876000 2949 7027 4 chr7D.!!$R2 4078
3 TraesCS7A01G457100 chr7D 566460717 566465791 5074 True 844.000000 2819 89.560400 4 2953 5 chr7D.!!$R3 2949
4 TraesCS7A01G457100 chr7B 620755473 620761252 5779 False 2704.333333 5192 94.213667 689 6390 3 chr7B.!!$F3 5701

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
401 402 0.947244 ACAGAGCTCAAACGCAAAGG 59.053 50.000 17.77 0.0 0.00 3.11 F
800 2651 1.157276 ACCACCTGCTCTCCAGAGT 59.843 57.895 5.49 0.0 44.64 3.24 F
1955 4527 0.882042 AGAGTTGTTGAGCCGTGCAG 60.882 55.000 0.00 0.0 0.00 4.41 F
2764 5441 1.133823 TCATGGCACCACTGTTTCTGT 60.134 47.619 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 4414 1.066858 AGGCACTCTATGTTGACCACG 60.067 52.381 0.00 0.00 0.00 4.94 R
2744 5421 1.133823 ACAGAAACAGTGGTGCCATGA 60.134 47.619 0.00 0.00 0.00 3.07 R
2773 5450 2.574006 AGCAAGGAGTGAAAGCATCA 57.426 45.000 0.00 0.00 35.05 3.07 R
6552 9310 7.170828 TGAATACAGCAAGTTATAACTATGCGG 59.829 37.037 28.76 28.76 42.46 5.69 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
42 43 8.973378 GCTACAAATGACTAAGTATCTCATGAC 58.027 37.037 0.00 0.00 0.00 3.06
67 68 7.143340 CACAACAAATATTATGAGCATCCAGG 58.857 38.462 0.00 0.00 0.00 4.45
93 94 8.706322 ACAATTATCTTTCAAACCTAAGGTGT 57.294 30.769 0.00 0.00 35.34 4.16
95 96 9.626045 CAATTATCTTTCAAACCTAAGGTGTTC 57.374 33.333 0.00 0.00 35.34 3.18
108 109 3.733443 AGGTGTTCTGTTTCATTTGGC 57.267 42.857 0.00 0.00 0.00 4.52
111 112 3.989817 GGTGTTCTGTTTCATTTGGCATC 59.010 43.478 0.00 0.00 0.00 3.91
114 115 5.176223 GTGTTCTGTTTCATTTGGCATCAAG 59.824 40.000 0.00 0.00 33.98 3.02
150 151 4.862641 AGGTTTGTCCATGCCTAATACT 57.137 40.909 0.00 0.00 39.02 2.12
151 152 5.193099 AGGTTTGTCCATGCCTAATACTT 57.807 39.130 0.00 0.00 39.02 2.24
152 153 6.321821 AGGTTTGTCCATGCCTAATACTTA 57.678 37.500 0.00 0.00 39.02 2.24
153 154 6.911308 AGGTTTGTCCATGCCTAATACTTAT 58.089 36.000 0.00 0.00 39.02 1.73
154 155 6.772716 AGGTTTGTCCATGCCTAATACTTATG 59.227 38.462 0.00 0.00 39.02 1.90
155 156 6.016276 GGTTTGTCCATGCCTAATACTTATGG 60.016 42.308 0.00 0.00 39.66 2.74
156 157 5.241403 TGTCCATGCCTAATACTTATGGG 57.759 43.478 0.00 0.00 38.98 4.00
157 158 4.663120 TGTCCATGCCTAATACTTATGGGT 59.337 41.667 0.00 0.00 38.98 4.51
158 159 5.133660 TGTCCATGCCTAATACTTATGGGTT 59.866 40.000 0.00 0.00 38.98 4.11
159 160 5.473504 GTCCATGCCTAATACTTATGGGTTG 59.526 44.000 0.00 0.00 38.98 3.77
160 161 4.766891 CCATGCCTAATACTTATGGGTTGG 59.233 45.833 0.00 0.00 35.71 3.77
161 162 4.447138 TGCCTAATACTTATGGGTTGGG 57.553 45.455 0.00 0.00 0.00 4.12
162 163 3.154710 GCCTAATACTTATGGGTTGGGC 58.845 50.000 6.79 6.79 40.24 5.36
163 164 3.435890 GCCTAATACTTATGGGTTGGGCA 60.436 47.826 13.62 0.00 44.60 5.36
165 166 4.104102 CCTAATACTTATGGGTTGGGCAGA 59.896 45.833 0.00 0.00 0.00 4.26
168 169 3.577805 ACTTATGGGTTGGGCAGATAC 57.422 47.619 0.00 0.00 0.00 2.24
169 170 2.849943 ACTTATGGGTTGGGCAGATACA 59.150 45.455 0.00 0.00 0.00 2.29
170 171 3.214328 CTTATGGGTTGGGCAGATACAC 58.786 50.000 0.00 0.00 0.00 2.90
171 172 0.998928 ATGGGTTGGGCAGATACACA 59.001 50.000 0.00 0.00 0.00 3.72
172 173 0.998928 TGGGTTGGGCAGATACACAT 59.001 50.000 0.00 0.00 0.00 3.21
173 174 2.200955 TGGGTTGGGCAGATACACATA 58.799 47.619 0.00 0.00 0.00 2.29
174 175 2.092646 TGGGTTGGGCAGATACACATAC 60.093 50.000 0.00 0.00 0.00 2.39
175 176 2.172717 GGGTTGGGCAGATACACATACT 59.827 50.000 0.00 0.00 0.00 2.12
176 177 3.371595 GGGTTGGGCAGATACACATACTT 60.372 47.826 0.00 0.00 0.00 2.24
177 178 4.270008 GGTTGGGCAGATACACATACTTT 58.730 43.478 0.00 0.00 0.00 2.66
178 179 4.335594 GGTTGGGCAGATACACATACTTTC 59.664 45.833 0.00 0.00 0.00 2.62
179 180 4.150897 TGGGCAGATACACATACTTTCC 57.849 45.455 0.00 0.00 0.00 3.13
180 181 3.521531 TGGGCAGATACACATACTTTCCA 59.478 43.478 0.00 0.00 0.00 3.53
181 182 3.877508 GGGCAGATACACATACTTTCCAC 59.122 47.826 0.00 0.00 0.00 4.02
182 183 4.513442 GGCAGATACACATACTTTCCACA 58.487 43.478 0.00 0.00 0.00 4.17
183 184 4.941263 GGCAGATACACATACTTTCCACAA 59.059 41.667 0.00 0.00 0.00 3.33
184 185 5.414454 GGCAGATACACATACTTTCCACAAA 59.586 40.000 0.00 0.00 0.00 2.83
185 186 6.072175 GGCAGATACACATACTTTCCACAAAA 60.072 38.462 0.00 0.00 0.00 2.44
186 187 7.367285 GCAGATACACATACTTTCCACAAAAA 58.633 34.615 0.00 0.00 0.00 1.94
218 219 2.158682 ACACATACTGCAACAGGGTTCA 60.159 45.455 0.00 0.00 35.51 3.18
233 234 8.834465 CAACAGGGTTCATCTTCTAGAATTATG 58.166 37.037 16.49 16.49 0.00 1.90
234 235 8.324191 ACAGGGTTCATCTTCTAGAATTATGA 57.676 34.615 19.39 19.39 0.00 2.15
235 236 8.772250 ACAGGGTTCATCTTCTAGAATTATGAA 58.228 33.333 25.23 25.23 33.74 2.57
261 262 9.705290 AAAAACAATTCACAACAGTACTTCTTT 57.295 25.926 0.00 0.00 0.00 2.52
313 314 7.122055 TCTGTTTCAACTTTGACATGTTACCTT 59.878 33.333 0.00 0.00 36.83 3.50
314 315 8.282455 TGTTTCAACTTTGACATGTTACCTTA 57.718 30.769 0.00 0.00 36.83 2.69
315 316 8.185505 TGTTTCAACTTTGACATGTTACCTTAC 58.814 33.333 0.00 0.00 36.83 2.34
316 317 6.870971 TCAACTTTGACATGTTACCTTACC 57.129 37.500 0.00 0.00 31.01 2.85
317 318 6.597562 TCAACTTTGACATGTTACCTTACCT 58.402 36.000 0.00 0.00 31.01 3.08
318 319 7.737869 TCAACTTTGACATGTTACCTTACCTA 58.262 34.615 0.00 0.00 31.01 3.08
319 320 7.876068 TCAACTTTGACATGTTACCTTACCTAG 59.124 37.037 0.00 0.00 31.01 3.02
320 321 7.312415 ACTTTGACATGTTACCTTACCTAGT 57.688 36.000 0.00 0.00 0.00 2.57
321 322 8.426569 ACTTTGACATGTTACCTTACCTAGTA 57.573 34.615 0.00 0.00 0.00 1.82
322 323 8.309656 ACTTTGACATGTTACCTTACCTAGTAC 58.690 37.037 0.00 0.00 0.00 2.73
323 324 8.426569 TTTGACATGTTACCTTACCTAGTACT 57.573 34.615 0.00 0.00 0.00 2.73
324 325 7.636150 TGACATGTTACCTTACCTAGTACTC 57.364 40.000 0.00 0.00 0.00 2.59
325 326 7.408543 TGACATGTTACCTTACCTAGTACTCT 58.591 38.462 0.00 0.00 0.00 3.24
326 327 7.892241 TGACATGTTACCTTACCTAGTACTCTT 59.108 37.037 0.00 0.00 0.00 2.85
327 328 8.064336 ACATGTTACCTTACCTAGTACTCTTG 57.936 38.462 0.00 0.00 0.00 3.02
328 329 7.892241 ACATGTTACCTTACCTAGTACTCTTGA 59.108 37.037 0.00 0.00 0.00 3.02
329 330 8.746530 CATGTTACCTTACCTAGTACTCTTGAA 58.253 37.037 0.00 0.00 0.00 2.69
330 331 8.115490 TGTTACCTTACCTAGTACTCTTGAAC 57.885 38.462 0.00 0.00 0.00 3.18
331 332 7.946776 TGTTACCTTACCTAGTACTCTTGAACT 59.053 37.037 0.00 0.00 0.00 3.01
332 333 9.454859 GTTACCTTACCTAGTACTCTTGAACTA 57.545 37.037 0.00 0.00 0.00 2.24
334 335 8.946797 ACCTTACCTAGTACTCTTGAACTAAA 57.053 34.615 0.00 0.00 0.00 1.85
335 336 9.372189 ACCTTACCTAGTACTCTTGAACTAAAA 57.628 33.333 0.00 0.00 0.00 1.52
336 337 9.636879 CCTTACCTAGTACTCTTGAACTAAAAC 57.363 37.037 0.00 0.00 0.00 2.43
337 338 9.636879 CTTACCTAGTACTCTTGAACTAAAACC 57.363 37.037 0.00 0.00 0.00 3.27
338 339 7.607615 ACCTAGTACTCTTGAACTAAAACCA 57.392 36.000 0.00 0.00 0.00 3.67
339 340 7.440198 ACCTAGTACTCTTGAACTAAAACCAC 58.560 38.462 0.00 0.00 0.00 4.16
340 341 6.585322 CCTAGTACTCTTGAACTAAAACCACG 59.415 42.308 0.00 0.00 0.00 4.94
341 342 6.152932 AGTACTCTTGAACTAAAACCACGA 57.847 37.500 0.00 0.00 0.00 4.35
342 343 5.981915 AGTACTCTTGAACTAAAACCACGAC 59.018 40.000 0.00 0.00 0.00 4.34
343 344 3.800506 ACTCTTGAACTAAAACCACGACG 59.199 43.478 0.00 0.00 0.00 5.12
344 345 4.044336 TCTTGAACTAAAACCACGACGA 57.956 40.909 0.00 0.00 0.00 4.20
345 346 4.046462 TCTTGAACTAAAACCACGACGAG 58.954 43.478 0.00 0.00 0.00 4.18
346 347 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
347 348 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
348 349 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
349 350 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
350 351 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
351 352 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
352 353 5.531634 ACTAAAACCACGACGAGTAAATCA 58.468 37.500 0.00 0.00 0.00 2.57
353 354 4.985044 AAAACCACGACGAGTAAATCAG 57.015 40.909 0.00 0.00 0.00 2.90
354 355 3.928727 AACCACGACGAGTAAATCAGA 57.071 42.857 0.00 0.00 0.00 3.27
355 356 3.928727 ACCACGACGAGTAAATCAGAA 57.071 42.857 0.00 0.00 0.00 3.02
356 357 4.451629 ACCACGACGAGTAAATCAGAAT 57.548 40.909 0.00 0.00 0.00 2.40
357 358 4.174009 ACCACGACGAGTAAATCAGAATG 58.826 43.478 0.00 0.00 37.54 2.67
358 359 3.551890 CCACGACGAGTAAATCAGAATGG 59.448 47.826 0.00 0.00 36.16 3.16
359 360 4.421058 CACGACGAGTAAATCAGAATGGA 58.579 43.478 0.00 0.00 36.16 3.41
360 361 4.500837 CACGACGAGTAAATCAGAATGGAG 59.499 45.833 0.00 0.00 36.16 3.86
361 362 4.045104 CGACGAGTAAATCAGAATGGAGG 58.955 47.826 0.00 0.00 36.16 4.30
362 363 4.372656 GACGAGTAAATCAGAATGGAGGG 58.627 47.826 0.00 0.00 36.16 4.30
363 364 4.030913 ACGAGTAAATCAGAATGGAGGGA 58.969 43.478 0.00 0.00 36.16 4.20
364 365 4.100189 ACGAGTAAATCAGAATGGAGGGAG 59.900 45.833 0.00 0.00 36.16 4.30
365 366 4.100189 CGAGTAAATCAGAATGGAGGGAGT 59.900 45.833 0.00 0.00 36.16 3.85
395 396 3.131396 ACCAGTAAACAGAGCTCAAACG 58.869 45.455 17.77 3.66 0.00 3.60
399 400 3.625764 AGTAAACAGAGCTCAAACGCAAA 59.374 39.130 17.77 0.00 0.00 3.68
401 402 0.947244 ACAGAGCTCAAACGCAAAGG 59.053 50.000 17.77 0.00 0.00 3.11
402 403 0.947244 CAGAGCTCAAACGCAAAGGT 59.053 50.000 17.77 0.00 0.00 3.50
403 404 1.334869 CAGAGCTCAAACGCAAAGGTT 59.665 47.619 17.77 0.00 0.00 3.50
404 405 2.548057 CAGAGCTCAAACGCAAAGGTTA 59.452 45.455 17.77 0.00 0.00 2.85
405 406 3.189287 CAGAGCTCAAACGCAAAGGTTAT 59.811 43.478 17.77 0.00 0.00 1.89
406 407 4.391830 CAGAGCTCAAACGCAAAGGTTATA 59.608 41.667 17.77 0.00 0.00 0.98
407 408 5.001232 AGAGCTCAAACGCAAAGGTTATAA 58.999 37.500 17.77 0.00 0.00 0.98
438 439 1.299976 GGCTCCAATCGTGAAGGGT 59.700 57.895 0.00 0.00 0.00 4.34
442 443 2.420129 GCTCCAATCGTGAAGGGTGTAT 60.420 50.000 0.00 0.00 0.00 2.29
474 475 5.014202 GCCCTTCCTGAACTTAATTAACCA 58.986 41.667 0.00 0.00 0.00 3.67
495 496 1.211212 TCTGATCCACCCATTCTGCAG 59.789 52.381 7.63 7.63 0.00 4.41
500 501 2.265367 TCCACCCATTCTGCAGTCTTA 58.735 47.619 14.67 0.00 0.00 2.10
561 562 4.747540 AGAGACATGAAGAGATCGATCG 57.252 45.455 19.33 9.36 0.00 3.69
567 568 4.279420 ACATGAAGAGATCGATCGATGGAA 59.721 41.667 33.86 13.83 34.60 3.53
582 583 3.879295 CGATGGAATGCACTTGGAAGTAT 59.121 43.478 0.00 0.00 37.08 2.12
646 647 1.814394 TGAATGGCATCAGAACACTGC 59.186 47.619 0.00 0.00 35.16 4.40
650 651 3.780925 GCATCAGAACACTGCCAAC 57.219 52.632 0.00 0.00 0.00 3.77
673 674 8.676401 CAACACTAACATGTGATGGATTATTGA 58.324 33.333 0.00 0.00 40.12 2.57
717 2548 4.513442 TGGCGATTACTGATTAGCAACTT 58.487 39.130 0.00 0.00 0.00 2.66
752 2583 2.113433 CATGTCCCAGCAGAGCAGC 61.113 63.158 0.00 0.00 0.00 5.25
793 2644 4.008933 GACCGCACCACCTGCTCT 62.009 66.667 0.00 0.00 44.64 4.09
794 2645 3.941657 GACCGCACCACCTGCTCTC 62.942 68.421 0.00 0.00 44.64 3.20
795 2646 4.767255 CCGCACCACCTGCTCTCC 62.767 72.222 0.00 0.00 44.64 3.71
796 2647 4.007644 CGCACCACCTGCTCTCCA 62.008 66.667 0.00 0.00 44.64 3.86
797 2648 2.046507 GCACCACCTGCTCTCCAG 60.047 66.667 0.00 0.00 43.33 3.86
798 2649 2.587247 GCACCACCTGCTCTCCAGA 61.587 63.158 0.00 0.00 44.64 3.86
799 2650 1.595882 CACCACCTGCTCTCCAGAG 59.404 63.158 0.00 0.00 44.64 3.35
800 2651 1.157276 ACCACCTGCTCTCCAGAGT 59.843 57.895 5.49 0.00 44.64 3.24
812 2673 2.240160 TCTCCAGAGTCCAGACTAGTCC 59.760 54.545 19.38 4.02 42.66 3.85
852 2713 4.874533 CCCGTACCCCTCCCCTCC 62.875 77.778 0.00 0.00 0.00 4.30
967 3041 2.543777 TCGAATCCCGAATCCCAATC 57.456 50.000 0.00 0.00 45.43 2.67
1357 3929 2.257409 GACCCACATCCTCGCCATGT 62.257 60.000 0.00 0.00 34.67 3.21
1359 3931 1.378882 CCCACATCCTCGCCATGTTG 61.379 60.000 0.00 0.00 31.83 3.33
1955 4527 0.882042 AGAGTTGTTGAGCCGTGCAG 60.882 55.000 0.00 0.00 0.00 4.41
2181 4753 2.038952 GGAGTATGAGGTATGCATGCCA 59.961 50.000 31.95 15.66 34.71 4.92
2196 4768 4.646040 TGCATGCCAGCTTTTATCTTGTAT 59.354 37.500 16.68 0.00 34.99 2.29
2197 4769 5.827267 TGCATGCCAGCTTTTATCTTGTATA 59.173 36.000 16.68 0.00 34.99 1.47
2204 4776 7.713073 GCCAGCTTTTATCTTGTATAGTCTCTT 59.287 37.037 0.00 0.00 0.00 2.85
2205 4777 9.039870 CCAGCTTTTATCTTGTATAGTCTCTTG 57.960 37.037 0.00 0.00 0.00 3.02
2254 4826 1.475280 CATGCTGTATTGCTGGCTGTT 59.525 47.619 0.00 0.00 0.00 3.16
2257 4829 2.487762 TGCTGTATTGCTGGCTGTTTAC 59.512 45.455 0.00 0.00 0.00 2.01
2264 4836 3.207265 TGCTGGCTGTTTACTGAGAAA 57.793 42.857 0.00 0.00 0.00 2.52
2445 5017 7.709182 AGTGGTTTTACTTTGGATGCTTTTTAC 59.291 33.333 0.00 0.00 0.00 2.01
2628 5202 6.939730 TGTGAATACAATAGCTTCCAAGACAA 59.060 34.615 0.00 0.00 32.88 3.18
2629 5203 7.094805 TGTGAATACAATAGCTTCCAAGACAAC 60.095 37.037 0.00 0.00 32.88 3.32
2694 5371 3.550820 TGCTTTCACTCCTTGCTTACAA 58.449 40.909 0.00 0.00 0.00 2.41
2695 5372 9.332719 TTGATGCTTTCACTCCTTGCTTACAAG 62.333 40.741 0.00 0.00 42.68 3.16
2747 5424 9.820725 TTTTTCATGTCTTCTGTTTCATTTCAT 57.179 25.926 0.00 0.00 0.00 2.57
2748 5425 8.806177 TTTCATGTCTTCTGTTTCATTTCATG 57.194 30.769 0.00 0.00 33.74 3.07
2749 5426 6.916440 TCATGTCTTCTGTTTCATTTCATGG 58.084 36.000 0.00 0.00 33.42 3.66
2750 5427 5.125100 TGTCTTCTGTTTCATTTCATGGC 57.875 39.130 0.00 0.00 0.00 4.40
2751 5428 4.583907 TGTCTTCTGTTTCATTTCATGGCA 59.416 37.500 0.00 0.00 0.00 4.92
2752 5429 4.919754 GTCTTCTGTTTCATTTCATGGCAC 59.080 41.667 0.00 0.00 0.00 5.01
2753 5430 3.940209 TCTGTTTCATTTCATGGCACC 57.060 42.857 0.00 0.00 0.00 5.01
2754 5431 3.229293 TCTGTTTCATTTCATGGCACCA 58.771 40.909 0.00 0.00 0.00 4.17
2755 5432 3.005684 TCTGTTTCATTTCATGGCACCAC 59.994 43.478 0.00 0.00 0.00 4.16
2756 5433 2.964464 TGTTTCATTTCATGGCACCACT 59.036 40.909 0.00 0.00 0.00 4.00
2757 5434 3.243805 TGTTTCATTTCATGGCACCACTG 60.244 43.478 0.00 0.00 0.00 3.66
2758 5435 2.291209 TCATTTCATGGCACCACTGT 57.709 45.000 0.00 0.00 0.00 3.55
2759 5436 2.596346 TCATTTCATGGCACCACTGTT 58.404 42.857 0.00 0.00 0.00 3.16
2760 5437 2.964464 TCATTTCATGGCACCACTGTTT 59.036 40.909 0.00 0.00 0.00 2.83
2761 5438 3.005684 TCATTTCATGGCACCACTGTTTC 59.994 43.478 0.00 0.00 0.00 2.78
2762 5439 2.363306 TTCATGGCACCACTGTTTCT 57.637 45.000 0.00 0.00 0.00 2.52
2763 5440 1.608055 TCATGGCACCACTGTTTCTG 58.392 50.000 0.00 0.00 0.00 3.02
2764 5441 1.133823 TCATGGCACCACTGTTTCTGT 60.134 47.619 0.00 0.00 0.00 3.41
2765 5442 2.105649 TCATGGCACCACTGTTTCTGTA 59.894 45.455 0.00 0.00 0.00 2.74
2766 5443 2.254546 TGGCACCACTGTTTCTGTAG 57.745 50.000 0.00 0.00 0.00 2.74
2767 5444 1.765904 TGGCACCACTGTTTCTGTAGA 59.234 47.619 0.00 0.00 0.00 2.59
2768 5445 2.171659 TGGCACCACTGTTTCTGTAGAA 59.828 45.455 0.00 0.00 0.00 2.10
2769 5446 2.548480 GGCACCACTGTTTCTGTAGAAC 59.452 50.000 0.00 0.00 33.13 3.01
2770 5447 2.548480 GCACCACTGTTTCTGTAGAACC 59.452 50.000 0.00 0.00 33.13 3.62
2771 5448 3.744530 GCACCACTGTTTCTGTAGAACCT 60.745 47.826 0.00 0.00 33.13 3.50
2772 5449 4.451900 CACCACTGTTTCTGTAGAACCTT 58.548 43.478 0.00 0.00 33.13 3.50
2773 5450 4.881850 CACCACTGTTTCTGTAGAACCTTT 59.118 41.667 0.00 0.00 33.13 3.11
2774 5451 4.881850 ACCACTGTTTCTGTAGAACCTTTG 59.118 41.667 0.00 0.00 33.13 2.77
2775 5452 5.123227 CCACTGTTTCTGTAGAACCTTTGA 58.877 41.667 0.00 0.00 33.13 2.69
2776 5453 5.765182 CCACTGTTTCTGTAGAACCTTTGAT 59.235 40.000 0.00 0.00 33.13 2.57
2777 5454 6.293626 CCACTGTTTCTGTAGAACCTTTGATG 60.294 42.308 0.00 0.00 33.13 3.07
2778 5455 5.239525 ACTGTTTCTGTAGAACCTTTGATGC 59.760 40.000 0.00 0.00 33.13 3.91
2779 5456 5.376625 TGTTTCTGTAGAACCTTTGATGCT 58.623 37.500 0.00 0.00 33.13 3.79
2780 5457 5.827797 TGTTTCTGTAGAACCTTTGATGCTT 59.172 36.000 0.00 0.00 33.13 3.91
2781 5458 6.321181 TGTTTCTGTAGAACCTTTGATGCTTT 59.679 34.615 0.00 0.00 33.13 3.51
2782 5459 6.560253 TTCTGTAGAACCTTTGATGCTTTC 57.440 37.500 0.00 0.00 0.00 2.62
2783 5460 5.620206 TCTGTAGAACCTTTGATGCTTTCA 58.380 37.500 0.00 0.00 0.00 2.69
2784 5461 5.470098 TCTGTAGAACCTTTGATGCTTTCAC 59.530 40.000 0.00 0.00 32.84 3.18
2785 5462 5.376625 TGTAGAACCTTTGATGCTTTCACT 58.623 37.500 0.00 0.00 32.84 3.41
2786 5463 5.470098 TGTAGAACCTTTGATGCTTTCACTC 59.530 40.000 0.00 0.00 32.84 3.51
2787 5464 3.823304 AGAACCTTTGATGCTTTCACTCC 59.177 43.478 0.00 0.00 32.84 3.85
2788 5465 3.515602 ACCTTTGATGCTTTCACTCCT 57.484 42.857 0.00 0.00 32.84 3.69
2789 5466 3.837355 ACCTTTGATGCTTTCACTCCTT 58.163 40.909 0.00 0.00 32.84 3.36
2790 5467 3.571401 ACCTTTGATGCTTTCACTCCTTG 59.429 43.478 0.00 0.00 32.84 3.61
2791 5468 3.572584 CTTTGATGCTTTCACTCCTTGC 58.427 45.455 0.00 0.00 32.84 4.01
2792 5469 2.574006 TGATGCTTTCACTCCTTGCT 57.426 45.000 0.00 0.00 0.00 3.91
2793 5470 2.867624 TGATGCTTTCACTCCTTGCTT 58.132 42.857 0.00 0.00 0.00 3.91
2794 5471 4.019792 TGATGCTTTCACTCCTTGCTTA 57.980 40.909 0.00 0.00 0.00 3.09
2795 5472 3.753272 TGATGCTTTCACTCCTTGCTTAC 59.247 43.478 0.00 0.00 0.00 2.34
2796 5473 3.207265 TGCTTTCACTCCTTGCTTACA 57.793 42.857 0.00 0.00 0.00 2.41
2797 5474 3.550820 TGCTTTCACTCCTTGCTTACAA 58.449 40.909 0.00 0.00 0.00 2.41
2798 5475 9.332719 TTGATGCTTTCACTCCTTGCTTACAAG 62.333 40.741 0.00 0.00 42.68 3.16
6552 9310 6.258068 GTGCAATGTATCTACTTACCAAGGAC 59.742 42.308 0.00 0.00 0.00 3.85
6565 9323 6.098695 ACTTACCAAGGACCGCATAGTTATAA 59.901 38.462 0.00 0.00 0.00 0.98
6573 9331 4.766375 ACCGCATAGTTATAACTTGCTGT 58.234 39.130 29.29 27.44 39.09 4.40
6617 9375 6.653740 TGATCAATGACCATAGATCTTCATGC 59.346 38.462 0.00 0.00 38.13 4.06
6684 10476 8.463930 TGATTTTATTGTGGTTTCACTCTCTT 57.536 30.769 0.00 0.00 43.94 2.85
6747 10539 9.136952 GAAGCAATTCTTTGAATATATCATGGC 57.863 33.333 0.00 0.00 38.03 4.40
6854 10668 4.961438 AAATGAAAAGGGAGTGCACAAT 57.039 36.364 21.04 0.00 0.00 2.71
6874 10688 5.870978 ACAATTTCTAATTTGTGGCAGATGC 59.129 36.000 0.00 0.00 34.87 3.91
6915 10729 3.435671 GGAAACCCTAAACATCACGAGTG 59.564 47.826 0.00 0.00 0.00 3.51
6921 10735 4.935205 CCCTAAACATCACGAGTGAAATCA 59.065 41.667 10.15 0.00 43.58 2.57
6922 10736 5.063944 CCCTAAACATCACGAGTGAAATCAG 59.936 44.000 10.15 4.60 43.58 2.90
6963 10777 2.445682 TATGGGGTTTTATTGCCGCT 57.554 45.000 0.00 0.00 38.37 5.52
6979 10793 0.951040 CGCTATGCCTTCGAATCCCC 60.951 60.000 0.00 0.00 0.00 4.81
6980 10794 0.398318 GCTATGCCTTCGAATCCCCT 59.602 55.000 0.00 0.00 0.00 4.79
6981 10795 1.623811 GCTATGCCTTCGAATCCCCTA 59.376 52.381 0.00 0.00 0.00 3.53
6982 10796 2.613223 GCTATGCCTTCGAATCCCCTAC 60.613 54.545 0.00 0.00 0.00 3.18
6983 10797 1.507140 ATGCCTTCGAATCCCCTACA 58.493 50.000 0.00 0.00 0.00 2.74
7033 10848 4.957684 AAAAGGTATATGAGGAGACGGG 57.042 45.455 0.00 0.00 0.00 5.28
7034 10849 1.926108 AGGTATATGAGGAGACGGGC 58.074 55.000 0.00 0.00 0.00 6.13
7035 10850 1.429687 AGGTATATGAGGAGACGGGCT 59.570 52.381 0.00 0.00 0.00 5.19
7036 10851 1.546476 GGTATATGAGGAGACGGGCTG 59.454 57.143 0.00 0.00 0.00 4.85
7037 10852 1.067495 GTATATGAGGAGACGGGCTGC 60.067 57.143 0.00 0.00 34.75 5.25
7038 10853 1.476007 ATATGAGGAGACGGGCTGCC 61.476 60.000 11.05 11.05 35.18 4.85
7049 10864 3.741325 GGCTGCCCCCTAAGAAGA 58.259 61.111 7.66 0.00 0.00 2.87
7050 10865 1.224870 GGCTGCCCCCTAAGAAGAC 59.775 63.158 7.66 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.343617 TGTAGCTGCCCTGTATCAAAAC 58.656 45.455 0.00 0.00 0.00 2.43
1 2 3.712016 TGTAGCTGCCCTGTATCAAAA 57.288 42.857 0.00 0.00 0.00 2.44
2 3 3.712016 TTGTAGCTGCCCTGTATCAAA 57.288 42.857 0.00 0.00 0.00 2.69
14 15 8.976471 CATGAGATACTTAGTCATTTGTAGCTG 58.024 37.037 0.00 0.00 32.74 4.24
42 43 7.013559 TCCTGGATGCTCATAATATTTGTTGTG 59.986 37.037 0.00 0.00 0.00 3.33
67 68 8.793592 ACACCTTAGGTTTGAAAGATAATTGTC 58.206 33.333 0.00 0.00 31.02 3.18
93 94 5.068855 TGTCTTGATGCCAAATGAAACAGAA 59.931 36.000 0.00 0.00 0.00 3.02
95 96 4.873817 TGTCTTGATGCCAAATGAAACAG 58.126 39.130 0.00 0.00 0.00 3.16
122 123 4.159557 AGGCATGGACAAACCTAAAATGT 58.840 39.130 0.00 0.00 39.86 2.71
150 151 2.578480 TGTGTATCTGCCCAACCCATAA 59.422 45.455 0.00 0.00 0.00 1.90
151 152 2.200955 TGTGTATCTGCCCAACCCATA 58.799 47.619 0.00 0.00 0.00 2.74
152 153 0.998928 TGTGTATCTGCCCAACCCAT 59.001 50.000 0.00 0.00 0.00 4.00
153 154 0.998928 ATGTGTATCTGCCCAACCCA 59.001 50.000 0.00 0.00 0.00 4.51
154 155 2.172717 AGTATGTGTATCTGCCCAACCC 59.827 50.000 0.00 0.00 0.00 4.11
155 156 3.560636 AGTATGTGTATCTGCCCAACC 57.439 47.619 0.00 0.00 0.00 3.77
156 157 4.335594 GGAAAGTATGTGTATCTGCCCAAC 59.664 45.833 0.00 0.00 0.00 3.77
157 158 4.018870 TGGAAAGTATGTGTATCTGCCCAA 60.019 41.667 0.00 0.00 0.00 4.12
158 159 3.521531 TGGAAAGTATGTGTATCTGCCCA 59.478 43.478 0.00 0.00 0.00 5.36
159 160 3.877508 GTGGAAAGTATGTGTATCTGCCC 59.122 47.826 0.00 0.00 0.00 5.36
160 161 4.513442 TGTGGAAAGTATGTGTATCTGCC 58.487 43.478 0.00 0.00 0.00 4.85
161 162 6.494893 TTTGTGGAAAGTATGTGTATCTGC 57.505 37.500 0.00 0.00 0.00 4.26
184 185 8.893727 GTTGCAGTATGTGTATCTATCCTTTTT 58.106 33.333 0.00 0.00 39.31 1.94
185 186 8.046708 TGTTGCAGTATGTGTATCTATCCTTTT 58.953 33.333 0.00 0.00 39.31 2.27
186 187 7.564793 TGTTGCAGTATGTGTATCTATCCTTT 58.435 34.615 0.00 0.00 39.31 3.11
187 188 7.124573 TGTTGCAGTATGTGTATCTATCCTT 57.875 36.000 0.00 0.00 39.31 3.36
188 189 6.239430 CCTGTTGCAGTATGTGTATCTATCCT 60.239 42.308 0.00 0.00 39.31 3.24
189 190 5.928839 CCTGTTGCAGTATGTGTATCTATCC 59.071 44.000 0.00 0.00 39.31 2.59
196 197 3.071747 TGAACCCTGTTGCAGTATGTGTA 59.928 43.478 0.00 0.00 39.31 2.90
235 236 9.705290 AAAGAAGTACTGTTGTGAATTGTTTTT 57.295 25.926 0.00 0.00 0.00 1.94
243 244 8.958119 ACAGATTAAAGAAGTACTGTTGTGAA 57.042 30.769 0.00 0.00 35.52 3.18
261 262 5.013079 ACATGAGTCCTGGAACAACAGATTA 59.987 40.000 0.00 0.00 40.97 1.75
270 271 2.037772 ACAGACACATGAGTCCTGGAAC 59.962 50.000 18.21 0.00 39.34 3.62
271 272 2.329267 ACAGACACATGAGTCCTGGAA 58.671 47.619 18.21 0.00 39.34 3.53
273 274 2.847327 AACAGACACATGAGTCCTGG 57.153 50.000 18.21 11.45 39.34 4.45
313 314 8.579863 GTGGTTTTAGTTCAAGAGTACTAGGTA 58.420 37.037 0.00 0.00 30.68 3.08
314 315 7.440198 GTGGTTTTAGTTCAAGAGTACTAGGT 58.560 38.462 0.00 0.00 30.68 3.08
315 316 6.585322 CGTGGTTTTAGTTCAAGAGTACTAGG 59.415 42.308 0.00 0.00 30.68 3.02
316 317 7.325579 GTCGTGGTTTTAGTTCAAGAGTACTAG 59.674 40.741 0.00 0.00 30.68 2.57
317 318 7.141363 GTCGTGGTTTTAGTTCAAGAGTACTA 58.859 38.462 0.00 0.00 0.00 1.82
318 319 5.981915 GTCGTGGTTTTAGTTCAAGAGTACT 59.018 40.000 0.00 0.00 0.00 2.73
319 320 5.108103 CGTCGTGGTTTTAGTTCAAGAGTAC 60.108 44.000 0.00 0.00 0.00 2.73
320 321 4.977963 CGTCGTGGTTTTAGTTCAAGAGTA 59.022 41.667 0.00 0.00 0.00 2.59
321 322 3.800506 CGTCGTGGTTTTAGTTCAAGAGT 59.199 43.478 0.00 0.00 0.00 3.24
322 323 4.046462 TCGTCGTGGTTTTAGTTCAAGAG 58.954 43.478 0.00 0.00 0.00 2.85
323 324 4.044336 TCGTCGTGGTTTTAGTTCAAGA 57.956 40.909 0.00 0.00 0.00 3.02
324 325 3.800506 ACTCGTCGTGGTTTTAGTTCAAG 59.199 43.478 0.00 0.00 0.00 3.02
325 326 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
326 327 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
327 328 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
328 329 5.984926 TGATTTACTCGTCGTGGTTTTAGTT 59.015 36.000 0.00 0.00 0.00 2.24
329 330 5.531634 TGATTTACTCGTCGTGGTTTTAGT 58.468 37.500 0.00 0.00 0.00 2.24
330 331 5.860182 TCTGATTTACTCGTCGTGGTTTTAG 59.140 40.000 0.00 0.00 0.00 1.85
331 332 5.771469 TCTGATTTACTCGTCGTGGTTTTA 58.229 37.500 0.00 0.00 0.00 1.52
332 333 4.624015 TCTGATTTACTCGTCGTGGTTTT 58.376 39.130 0.00 0.00 0.00 2.43
333 334 4.247267 TCTGATTTACTCGTCGTGGTTT 57.753 40.909 0.00 0.00 0.00 3.27
334 335 3.928727 TCTGATTTACTCGTCGTGGTT 57.071 42.857 0.00 0.00 0.00 3.67
335 336 3.928727 TTCTGATTTACTCGTCGTGGT 57.071 42.857 0.00 0.00 0.00 4.16
336 337 3.551890 CCATTCTGATTTACTCGTCGTGG 59.448 47.826 0.00 0.00 0.00 4.94
337 338 4.421058 TCCATTCTGATTTACTCGTCGTG 58.579 43.478 0.00 0.00 0.00 4.35
338 339 4.440250 CCTCCATTCTGATTTACTCGTCGT 60.440 45.833 0.00 0.00 0.00 4.34
339 340 4.045104 CCTCCATTCTGATTTACTCGTCG 58.955 47.826 0.00 0.00 0.00 5.12
340 341 4.099573 TCCCTCCATTCTGATTTACTCGTC 59.900 45.833 0.00 0.00 0.00 4.20
341 342 4.030913 TCCCTCCATTCTGATTTACTCGT 58.969 43.478 0.00 0.00 0.00 4.18
342 343 4.100189 ACTCCCTCCATTCTGATTTACTCG 59.900 45.833 0.00 0.00 0.00 4.18
343 344 5.622346 ACTCCCTCCATTCTGATTTACTC 57.378 43.478 0.00 0.00 0.00 2.59
344 345 5.964477 TGTACTCCCTCCATTCTGATTTACT 59.036 40.000 0.00 0.00 0.00 2.24
345 346 6.235231 TGTACTCCCTCCATTCTGATTTAC 57.765 41.667 0.00 0.00 0.00 2.01
346 347 6.615316 TGATGTACTCCCTCCATTCTGATTTA 59.385 38.462 0.00 0.00 0.00 1.40
347 348 5.429762 TGATGTACTCCCTCCATTCTGATTT 59.570 40.000 0.00 0.00 0.00 2.17
348 349 4.971282 TGATGTACTCCCTCCATTCTGATT 59.029 41.667 0.00 0.00 0.00 2.57
349 350 4.560739 TGATGTACTCCCTCCATTCTGAT 58.439 43.478 0.00 0.00 0.00 2.90
350 351 3.994317 TGATGTACTCCCTCCATTCTGA 58.006 45.455 0.00 0.00 0.00 3.27
351 352 4.760530 TTGATGTACTCCCTCCATTCTG 57.239 45.455 0.00 0.00 0.00 3.02
352 353 5.308237 GGTATTGATGTACTCCCTCCATTCT 59.692 44.000 0.00 0.00 0.00 2.40
353 354 5.071788 TGGTATTGATGTACTCCCTCCATTC 59.928 44.000 0.00 0.00 0.00 2.67
354 355 4.975147 TGGTATTGATGTACTCCCTCCATT 59.025 41.667 0.00 0.00 0.00 3.16
355 356 4.566837 TGGTATTGATGTACTCCCTCCAT 58.433 43.478 0.00 0.00 0.00 3.41
356 357 3.967326 CTGGTATTGATGTACTCCCTCCA 59.033 47.826 0.00 0.00 0.00 3.86
357 358 3.967987 ACTGGTATTGATGTACTCCCTCC 59.032 47.826 0.00 0.00 0.00 4.30
358 359 6.726490 TTACTGGTATTGATGTACTCCCTC 57.274 41.667 0.00 0.00 0.00 4.30
359 360 6.442564 TGTTTACTGGTATTGATGTACTCCCT 59.557 38.462 0.00 0.00 0.00 4.20
360 361 6.646267 TGTTTACTGGTATTGATGTACTCCC 58.354 40.000 0.00 0.00 0.00 4.30
361 362 7.553334 TCTGTTTACTGGTATTGATGTACTCC 58.447 38.462 0.00 0.00 0.00 3.85
362 363 7.222999 GCTCTGTTTACTGGTATTGATGTACTC 59.777 40.741 0.00 0.00 0.00 2.59
363 364 7.042335 GCTCTGTTTACTGGTATTGATGTACT 58.958 38.462 0.00 0.00 0.00 2.73
364 365 7.042335 AGCTCTGTTTACTGGTATTGATGTAC 58.958 38.462 0.00 0.00 0.00 2.90
365 366 7.093509 TGAGCTCTGTTTACTGGTATTGATGTA 60.094 37.037 16.19 0.00 0.00 2.29
395 396 6.701400 CCTTGCCACATAATTATAACCTTTGC 59.299 38.462 0.00 0.00 0.00 3.68
399 400 4.832823 GCCCTTGCCACATAATTATAACCT 59.167 41.667 0.00 0.00 0.00 3.50
401 402 5.048013 GGAGCCCTTGCCACATAATTATAAC 60.048 44.000 0.00 0.00 38.69 1.89
402 403 5.076873 GGAGCCCTTGCCACATAATTATAA 58.923 41.667 0.00 0.00 38.69 0.98
403 404 4.105537 TGGAGCCCTTGCCACATAATTATA 59.894 41.667 0.00 0.00 38.69 0.98
404 405 3.117169 TGGAGCCCTTGCCACATAATTAT 60.117 43.478 0.00 0.00 38.69 1.28
405 406 2.243478 TGGAGCCCTTGCCACATAATTA 59.757 45.455 0.00 0.00 38.69 1.40
406 407 1.006998 TGGAGCCCTTGCCACATAATT 59.993 47.619 0.00 0.00 38.69 1.40
407 408 0.630673 TGGAGCCCTTGCCACATAAT 59.369 50.000 0.00 0.00 38.69 1.28
474 475 1.848388 TGCAGAATGGGTGGATCAGAT 59.152 47.619 0.00 0.00 35.86 2.90
515 516 4.882559 TCCATCAGCCTCCCAATATTTTT 58.117 39.130 0.00 0.00 0.00 1.94
525 526 2.968574 TGTCTCTTATCCATCAGCCTCC 59.031 50.000 0.00 0.00 0.00 4.30
531 532 7.309073 CGATCTCTTCATGTCTCTTATCCATCA 60.309 40.741 0.00 0.00 0.00 3.07
534 535 6.064717 TCGATCTCTTCATGTCTCTTATCCA 58.935 40.000 0.00 0.00 0.00 3.41
535 536 6.567687 TCGATCTCTTCATGTCTCTTATCC 57.432 41.667 0.00 0.00 0.00 2.59
561 562 6.291377 TCTATACTTCCAAGTGCATTCCATC 58.709 40.000 2.01 0.00 40.07 3.51
567 568 7.831193 AGTTTTGATCTATACTTCCAAGTGCAT 59.169 33.333 2.01 0.00 40.07 3.96
582 583 4.811969 TGTTCGGGCTAGTTTTGATCTA 57.188 40.909 0.00 0.00 0.00 1.98
717 2548 2.639347 ACATGACTGACTGGTCCAATGA 59.361 45.455 0.00 0.00 35.54 2.57
752 2583 2.644992 GTTTTGCTGGCCCTGTCG 59.355 61.111 0.00 0.00 0.00 4.35
792 2643 2.241176 AGGACTAGTCTGGACTCTGGAG 59.759 54.545 21.88 2.09 42.54 3.86
793 2644 2.240160 GAGGACTAGTCTGGACTCTGGA 59.760 54.545 21.88 0.00 42.54 3.86
794 2645 2.650322 GAGGACTAGTCTGGACTCTGG 58.350 57.143 21.88 2.43 42.54 3.86
795 2646 2.285083 CGAGGACTAGTCTGGACTCTG 58.715 57.143 21.88 11.73 42.54 3.35
796 2647 1.407712 GCGAGGACTAGTCTGGACTCT 60.408 57.143 21.88 9.59 42.54 3.24
797 2648 1.018910 GCGAGGACTAGTCTGGACTC 58.981 60.000 21.88 17.28 42.54 3.36
798 2649 0.394625 GGCGAGGACTAGTCTGGACT 60.395 60.000 21.88 10.68 45.02 3.85
799 2650 1.385756 GGGCGAGGACTAGTCTGGAC 61.386 65.000 21.88 13.12 0.00 4.02
800 2651 1.076923 GGGCGAGGACTAGTCTGGA 60.077 63.158 21.88 0.00 0.00 3.86
936 2797 4.246206 ATTCGATCGACGCGGCGA 62.246 61.111 41.52 41.52 45.22 5.54
1023 3595 4.265056 ACCAGGGTGTCGTTGCCC 62.265 66.667 0.00 0.00 45.16 5.36
1167 3739 4.760220 AAGGGGGCGTGGGAGGAT 62.760 66.667 0.00 0.00 0.00 3.24
1642 4214 2.511600 CACCTTCATCCCGGACGC 60.512 66.667 0.73 0.00 0.00 5.19
1842 4414 1.066858 AGGCACTCTATGTTGACCACG 60.067 52.381 0.00 0.00 0.00 4.94
1878 4450 2.737180 CGGATCATCCCCCTCACG 59.263 66.667 0.00 0.00 31.13 4.35
1957 4529 2.203056 TGAATCTGCCATCGCCCG 60.203 61.111 0.00 0.00 0.00 6.13
2204 4776 9.811995 CAAGTACCACACTAAGCTTATATAACA 57.188 33.333 6.64 0.00 36.04 2.41
2254 4826 6.183360 ACACCAAATGCAACATTTCTCAGTAA 60.183 34.615 2.65 0.00 0.00 2.24
2257 4829 4.624015 ACACCAAATGCAACATTTCTCAG 58.376 39.130 2.65 0.00 0.00 3.35
2264 4836 5.011943 ACCTGAAATACACCAAATGCAACAT 59.988 36.000 0.00 0.00 0.00 2.71
2417 4989 3.573967 AGCATCCAAAGTAAAACCACTGG 59.426 43.478 0.00 0.00 0.00 4.00
2445 5017 1.667724 GGCAGTTCATTCTCATCCACG 59.332 52.381 0.00 0.00 0.00 4.94
2591 5163 8.715998 GCTATTGTATTCACATGGAGATAACAG 58.284 37.037 0.00 0.00 33.76 3.16
2721 5398 9.820725 ATGAAATGAAACAGAAGACATGAAAAA 57.179 25.926 0.00 0.00 0.00 1.94
2740 5417 3.006110 AGAAACAGTGGTGCCATGAAATG 59.994 43.478 0.00 0.00 46.21 2.32
2741 5418 3.006110 CAGAAACAGTGGTGCCATGAAAT 59.994 43.478 0.00 0.00 0.00 2.17
2742 5419 2.361757 CAGAAACAGTGGTGCCATGAAA 59.638 45.455 0.00 0.00 0.00 2.69
2743 5420 1.955778 CAGAAACAGTGGTGCCATGAA 59.044 47.619 0.00 0.00 0.00 2.57
2744 5421 1.133823 ACAGAAACAGTGGTGCCATGA 60.134 47.619 0.00 0.00 0.00 3.07
2745 5422 1.321474 ACAGAAACAGTGGTGCCATG 58.679 50.000 0.00 0.00 0.00 3.66
2746 5423 2.371841 TCTACAGAAACAGTGGTGCCAT 59.628 45.455 0.00 0.00 0.00 4.40
2747 5424 1.765904 TCTACAGAAACAGTGGTGCCA 59.234 47.619 0.00 0.00 0.00 4.92
2748 5425 2.543777 TCTACAGAAACAGTGGTGCC 57.456 50.000 0.00 0.00 0.00 5.01
2749 5426 2.548480 GGTTCTACAGAAACAGTGGTGC 59.452 50.000 2.09 0.00 41.25 5.01
2750 5427 4.073293 AGGTTCTACAGAAACAGTGGTG 57.927 45.455 9.57 0.00 43.92 4.17
2751 5428 4.772886 AAGGTTCTACAGAAACAGTGGT 57.227 40.909 9.57 0.00 43.92 4.16
2752 5429 5.123227 TCAAAGGTTCTACAGAAACAGTGG 58.877 41.667 9.57 0.00 43.92 4.00
2753 5430 6.662616 CATCAAAGGTTCTACAGAAACAGTG 58.337 40.000 9.57 6.68 43.92 3.66
2754 5431 5.239525 GCATCAAAGGTTCTACAGAAACAGT 59.760 40.000 9.57 0.00 43.92 3.55
2755 5432 5.471456 AGCATCAAAGGTTCTACAGAAACAG 59.529 40.000 9.57 0.00 43.92 3.16
2756 5433 5.376625 AGCATCAAAGGTTCTACAGAAACA 58.623 37.500 9.57 0.00 43.92 2.83
2757 5434 5.948992 AGCATCAAAGGTTCTACAGAAAC 57.051 39.130 0.00 0.00 41.89 2.78
2758 5435 6.545666 TGAAAGCATCAAAGGTTCTACAGAAA 59.454 34.615 0.00 0.00 33.42 2.52
2759 5436 6.017109 GTGAAAGCATCAAAGGTTCTACAGAA 60.017 38.462 0.00 0.00 40.50 3.02
2760 5437 5.470098 GTGAAAGCATCAAAGGTTCTACAGA 59.530 40.000 0.00 0.00 40.50 3.41
2761 5438 5.471456 AGTGAAAGCATCAAAGGTTCTACAG 59.529 40.000 0.00 0.00 40.50 2.74
2762 5439 5.376625 AGTGAAAGCATCAAAGGTTCTACA 58.623 37.500 0.00 0.00 40.50 2.74
2763 5440 5.106515 GGAGTGAAAGCATCAAAGGTTCTAC 60.107 44.000 0.00 0.00 40.50 2.59
2764 5441 5.003804 GGAGTGAAAGCATCAAAGGTTCTA 58.996 41.667 0.00 0.00 40.50 2.10
2765 5442 3.823304 GGAGTGAAAGCATCAAAGGTTCT 59.177 43.478 0.00 0.00 40.50 3.01
2766 5443 3.823304 AGGAGTGAAAGCATCAAAGGTTC 59.177 43.478 0.00 0.00 40.50 3.62
2767 5444 3.837355 AGGAGTGAAAGCATCAAAGGTT 58.163 40.909 0.00 0.00 40.50 3.50
2768 5445 3.515602 AGGAGTGAAAGCATCAAAGGT 57.484 42.857 0.00 0.00 40.50 3.50
2769 5446 3.613432 GCAAGGAGTGAAAGCATCAAAGG 60.613 47.826 0.00 0.00 40.50 3.11
2770 5447 3.255149 AGCAAGGAGTGAAAGCATCAAAG 59.745 43.478 0.00 0.00 40.50 2.77
2771 5448 3.225104 AGCAAGGAGTGAAAGCATCAAA 58.775 40.909 0.00 0.00 40.50 2.69
2772 5449 2.867624 AGCAAGGAGTGAAAGCATCAA 58.132 42.857 0.00 0.00 40.50 2.57
2773 5450 2.574006 AGCAAGGAGTGAAAGCATCA 57.426 45.000 0.00 0.00 35.05 3.07
2774 5451 3.753272 TGTAAGCAAGGAGTGAAAGCATC 59.247 43.478 0.00 0.00 0.00 3.91
2775 5452 3.754965 TGTAAGCAAGGAGTGAAAGCAT 58.245 40.909 0.00 0.00 0.00 3.79
2776 5453 3.207265 TGTAAGCAAGGAGTGAAAGCA 57.793 42.857 0.00 0.00 0.00 3.91
2777 5454 4.152607 CTTGTAAGCAAGGAGTGAAAGC 57.847 45.455 0.00 0.00 46.17 3.51
6552 9310 7.170828 TGAATACAGCAAGTTATAACTATGCGG 59.829 37.037 28.76 28.76 42.46 5.69
6565 9323 6.653020 TCTTCCATACATGAATACAGCAAGT 58.347 36.000 0.00 0.00 0.00 3.16
6617 9375 5.342433 TCTCACTGCAACAAAACATTCAAG 58.658 37.500 0.00 0.00 0.00 3.02
6700 10492 8.845227 TGCTTCTCATCTAACATTAAACAAACA 58.155 29.630 0.00 0.00 0.00 2.83
6760 10552 6.704289 AGCACAATATGATTGTAAGCACAT 57.296 33.333 13.77 0.00 33.76 3.21
6770 10566 8.076910 TCCCACAAAAATAGCACAATATGATT 57.923 30.769 0.00 0.00 0.00 2.57
6780 10576 3.386078 TGCACTTTCCCACAAAAATAGCA 59.614 39.130 0.00 0.00 0.00 3.49
6892 10706 3.007635 CTCGTGATGTTTAGGGTTTCCC 58.992 50.000 0.00 0.00 45.90 3.97
6894 10708 4.312443 TCACTCGTGATGTTTAGGGTTTC 58.688 43.478 0.00 0.00 34.14 2.78
6897 10711 4.345859 TTTCACTCGTGATGTTTAGGGT 57.654 40.909 0.00 0.00 39.64 4.34
6899 10713 5.869344 TCTGATTTCACTCGTGATGTTTAGG 59.131 40.000 0.00 0.00 39.64 2.69
6900 10714 6.951256 TCTGATTTCACTCGTGATGTTTAG 57.049 37.500 0.00 0.00 39.64 1.85
6913 10727 8.330302 CAACCAAGTCAATTTTTCTGATTTCAC 58.670 33.333 0.00 0.00 0.00 3.18
6915 10729 7.710475 TCCAACCAAGTCAATTTTTCTGATTTC 59.290 33.333 0.00 0.00 0.00 2.17
6921 10735 9.492973 CATATTTCCAACCAAGTCAATTTTTCT 57.507 29.630 0.00 0.00 0.00 2.52
6922 10736 8.720562 CCATATTTCCAACCAAGTCAATTTTTC 58.279 33.333 0.00 0.00 0.00 2.29
6963 10777 2.632996 CTGTAGGGGATTCGAAGGCATA 59.367 50.000 3.35 0.00 0.00 3.14
6979 10793 1.759445 CACCCTCTCCATGTCCTGTAG 59.241 57.143 0.00 0.00 0.00 2.74
6980 10794 1.866015 CACCCTCTCCATGTCCTGTA 58.134 55.000 0.00 0.00 0.00 2.74
6981 10795 1.557269 GCACCCTCTCCATGTCCTGT 61.557 60.000 0.00 0.00 0.00 4.00
6982 10796 1.222936 GCACCCTCTCCATGTCCTG 59.777 63.158 0.00 0.00 0.00 3.86
6983 10797 0.548682 AAGCACCCTCTCCATGTCCT 60.549 55.000 0.00 0.00 0.00 3.85
7027 10842 4.733725 TTAGGGGGCAGCCCGTCT 62.734 66.667 25.18 24.25 46.66 4.18
7028 10843 4.176752 CTTAGGGGGCAGCCCGTC 62.177 72.222 25.18 18.56 46.66 4.79
7029 10844 4.733725 TCTTAGGGGGCAGCCCGT 62.734 66.667 25.18 16.57 46.66 5.28
7030 10845 3.406595 CTTCTTAGGGGGCAGCCCG 62.407 68.421 25.18 10.33 46.66 6.13
7031 10846 2.001269 TCTTCTTAGGGGGCAGCCC 61.001 63.158 24.23 24.23 44.51 5.19
7032 10847 1.224870 GTCTTCTTAGGGGGCAGCC 59.775 63.158 1.26 1.26 0.00 4.85
7033 10848 4.966123 GTCTTCTTAGGGGGCAGC 57.034 61.111 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.