Multiple sequence alignment - TraesCS7B01G092500

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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 TraesCS7B01G092500 chr7B 100.000 5069 0 0 1 5069 105885402 105880334 0.000000e+00 9361.0
1 TraesCS7B01G092500 chr7B 88.764 445 42 6 3 445 498369400 498369838 5.770000e-149 538.0
2 TraesCS7B01G092500 chr7D 95.657 4559 139 23 545 5065 140806375 140801838 0.000000e+00 7267.0
3 TraesCS7B01G092500 chr7D 91.762 437 29 5 1 435 607122997 607123428 7.260000e-168 601.0
4 TraesCS7B01G092500 chr7D 89.703 437 38 5 1 435 566543384 566543815 7.420000e-153 551.0
5 TraesCS7B01G092500 chr7D 93.750 64 4 0 3617 3680 511117079 511117016 4.180000e-16 97.1
6 TraesCS7B01G092500 chr7A 95.094 3975 127 22 545 4482 142986607 142982664 0.000000e+00 6198.0
7 TraesCS7B01G092500 chr7A 88.915 424 41 4 4 425 708909378 708908959 7.520000e-143 518.0
8 TraesCS7B01G092500 chr7A 97.674 86 2 0 4980 5065 142982591 142982506 1.140000e-31 148.0
9 TraesCS7B01G092500 chr6A 78.020 1101 201 25 1193 2275 541229104 541228027 0.000000e+00 654.0
10 TraesCS7B01G092500 chr6D 78.035 1079 199 24 1181 2243 394724283 394725339 0.000000e+00 645.0
11 TraesCS7B01G092500 chr6D 88.158 304 35 1 3422 3725 73792611 73792913 1.340000e-95 361.0
12 TraesCS7B01G092500 chr6B 78.015 1078 197 26 1193 2253 590913506 590912452 4.280000e-180 641.0
13 TraesCS7B01G092500 chr6B 79.119 613 69 36 3419 4012 564364819 564364247 8.020000e-98 368.0
14 TraesCS7B01G092500 chr1B 91.055 436 33 4 4 438 117210531 117210101 7.310000e-163 584.0
15 TraesCS7B01G092500 chr1B 84.906 212 22 5 3422 3633 577972142 577972343 6.650000e-49 206.0
16 TraesCS7B01G092500 chr5B 90.618 437 34 5 1 435 254978639 254979070 1.580000e-159 573.0
17 TraesCS7B01G092500 chr5B 87.810 443 29 9 1 442 455346703 455347121 3.530000e-136 496.0
18 TraesCS7B01G092500 chr5B 80.168 595 73 27 3431 4012 2053846 2053284 2.200000e-108 403.0
19 TraesCS7B01G092500 chr4B 89.931 437 37 5 4 438 167945860 167945429 1.590000e-154 556.0
20 TraesCS7B01G092500 chr3B 89.757 371 30 6 77 446 678536205 678535842 7.680000e-128 468.0
21 TraesCS7B01G092500 chr2D 80.565 602 61 27 3428 4012 81653498 81654060 3.650000e-111 412.0
22 TraesCS7B01G092500 chr5D 83.721 215 25 5 3422 3636 277314234 277314030 1.440000e-45 195.0
23 TraesCS7B01G092500 chr4D 95.385 65 0 3 437 500 473824210 473824272 3.230000e-17 100.0


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 TraesCS7B01G092500 chr7B 105880334 105885402 5068 True 9361 9361 100.000 1 5069 1 chr7B.!!$R1 5068
1 TraesCS7B01G092500 chr7D 140801838 140806375 4537 True 7267 7267 95.657 545 5065 1 chr7D.!!$R1 4520
2 TraesCS7B01G092500 chr7A 142982506 142986607 4101 True 3173 6198 96.384 545 5065 2 chr7A.!!$R2 4520
3 TraesCS7B01G092500 chr6A 541228027 541229104 1077 True 654 654 78.020 1193 2275 1 chr6A.!!$R1 1082
4 TraesCS7B01G092500 chr6D 394724283 394725339 1056 False 645 645 78.035 1181 2243 1 chr6D.!!$F2 1062
5 TraesCS7B01G092500 chr6B 590912452 590913506 1054 True 641 641 78.015 1193 2253 1 chr6B.!!$R2 1060
6 TraesCS7B01G092500 chr6B 564364247 564364819 572 True 368 368 79.119 3419 4012 1 chr6B.!!$R1 593
7 TraesCS7B01G092500 chr5B 2053284 2053846 562 True 403 403 80.168 3431 4012 1 chr5B.!!$R1 581
8 TraesCS7B01G092500 chr2D 81653498 81654060 562 False 412 412 80.565 3428 4012 1 chr2D.!!$F1 584

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
447 448 0.030603 GGGGGTCAGGAGAGAGGATT 60.031 60.0 0.00 0.0 0.00 3.01 F
1880 1898 0.106619 ATCGCCTACTCCGACTTCCT 60.107 55.0 0.00 0.0 37.56 3.36 F
1887 1905 0.969894 ACTCCGACTTCCTGTTCCTG 59.030 55.0 0.00 0.0 0.00 3.86 F
3579 3640 0.911045 TCCAAGCATCAGCCCTGAGA 60.911 55.0 4.16 0.0 43.61 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2100 1.227527 CATCTCCACGGCGCCATTA 60.228 57.895 28.98 7.46 0.00 1.90 R
3579 3640 0.253044 ACTGCAGCACCACGGATAAT 59.747 50.000 15.27 0.00 0.00 1.28 R
3608 3669 4.312443 GCCATGGCTTCATATTTCCATTG 58.688 43.478 29.98 0.00 37.22 2.82 R
4739 4832 2.092291 ATGGTGCGCAACGTAGACG 61.092 57.895 20.83 0.00 46.33 4.18 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
19 20 4.715523 GCCGCTAGCCAACCACCA 62.716 66.667 9.66 0.00 34.35 4.17
20 21 2.746277 CCGCTAGCCAACCACCAC 60.746 66.667 9.66 0.00 0.00 4.16
21 22 2.746277 CGCTAGCCAACCACCACC 60.746 66.667 9.66 0.00 0.00 4.61
22 23 2.746277 GCTAGCCAACCACCACCG 60.746 66.667 2.29 0.00 0.00 4.94
23 24 2.046314 CTAGCCAACCACCACCGG 60.046 66.667 0.00 0.00 0.00 5.28
24 25 3.622060 CTAGCCAACCACCACCGGG 62.622 68.421 6.32 0.00 41.29 5.73
32 33 4.436998 CACCACCGGGAGCGAGTC 62.437 72.222 6.32 0.00 38.05 3.36
44 45 4.426112 CGAGTCGCAGCAGAGCCA 62.426 66.667 0.00 0.00 0.00 4.75
45 46 2.813042 GAGTCGCAGCAGAGCCAC 60.813 66.667 0.00 0.00 0.00 5.01
46 47 4.731612 AGTCGCAGCAGAGCCACG 62.732 66.667 0.00 0.00 30.59 4.94
50 51 4.704833 GCAGCAGAGCCACGGGAA 62.705 66.667 0.00 0.00 0.00 3.97
51 52 2.743928 CAGCAGAGCCACGGGAAC 60.744 66.667 0.00 0.00 0.00 3.62
52 53 3.241530 AGCAGAGCCACGGGAACA 61.242 61.111 0.00 0.00 0.00 3.18
53 54 3.050275 GCAGAGCCACGGGAACAC 61.050 66.667 0.00 0.00 0.00 3.32
54 55 2.358737 CAGAGCCACGGGAACACC 60.359 66.667 0.00 0.00 0.00 4.16
55 56 2.847234 AGAGCCACGGGAACACCA 60.847 61.111 0.00 0.00 40.22 4.17
56 57 2.668550 GAGCCACGGGAACACCAC 60.669 66.667 0.00 0.00 40.22 4.16
57 58 3.168528 AGCCACGGGAACACCACT 61.169 61.111 0.00 0.00 40.22 4.00
58 59 2.668550 GCCACGGGAACACCACTC 60.669 66.667 0.00 0.00 40.22 3.51
59 60 2.032071 CCACGGGAACACCACTCC 59.968 66.667 0.00 0.00 40.22 3.85
60 61 2.813726 CCACGGGAACACCACTCCA 61.814 63.158 0.00 0.00 40.22 3.86
61 62 1.374947 CACGGGAACACCACTCCAT 59.625 57.895 0.00 0.00 40.22 3.41
62 63 0.955428 CACGGGAACACCACTCCATG 60.955 60.000 0.00 0.00 40.22 3.66
63 64 2.040544 CGGGAACACCACTCCATGC 61.041 63.158 0.00 0.00 40.22 4.06
64 65 1.678970 GGGAACACCACTCCATGCC 60.679 63.158 0.00 0.00 39.85 4.40
65 66 1.380302 GGAACACCACTCCATGCCT 59.620 57.895 0.00 0.00 32.77 4.75
66 67 0.618458 GGAACACCACTCCATGCCTA 59.382 55.000 0.00 0.00 32.77 3.93
67 68 1.004277 GGAACACCACTCCATGCCTAA 59.996 52.381 0.00 0.00 32.77 2.69
68 69 2.084546 GAACACCACTCCATGCCTAAC 58.915 52.381 0.00 0.00 0.00 2.34
69 70 1.064003 ACACCACTCCATGCCTAACA 58.936 50.000 0.00 0.00 0.00 2.41
70 71 1.003580 ACACCACTCCATGCCTAACAG 59.996 52.381 0.00 0.00 0.00 3.16
71 72 1.278985 CACCACTCCATGCCTAACAGA 59.721 52.381 0.00 0.00 0.00 3.41
72 73 1.556911 ACCACTCCATGCCTAACAGAG 59.443 52.381 0.00 0.00 0.00 3.35
89 90 2.281970 GGTCACAACCCCGAACCC 60.282 66.667 0.00 0.00 39.93 4.11
90 91 2.281970 GTCACAACCCCGAACCCC 60.282 66.667 0.00 0.00 0.00 4.95
91 92 3.943691 TCACAACCCCGAACCCCG 61.944 66.667 0.00 0.00 38.18 5.73
109 110 4.113815 CCGCCCAGATCCAGCCAA 62.114 66.667 0.00 0.00 0.00 4.52
110 111 2.515523 CGCCCAGATCCAGCCAAG 60.516 66.667 0.00 0.00 0.00 3.61
111 112 2.123982 GCCCAGATCCAGCCAAGG 60.124 66.667 0.00 0.00 0.00 3.61
112 113 2.988839 GCCCAGATCCAGCCAAGGT 61.989 63.158 0.00 0.00 0.00 3.50
113 114 1.077212 CCCAGATCCAGCCAAGGTG 60.077 63.158 0.00 0.00 0.00 4.00
120 121 3.089838 CAGCCAAGGTGGATCCCA 58.910 61.111 9.90 0.00 40.96 4.37
121 122 1.077212 CAGCCAAGGTGGATCCCAG 60.077 63.158 9.90 0.00 40.96 4.45
122 123 2.276740 GCCAAGGTGGATCCCAGG 59.723 66.667 9.90 5.02 40.96 4.45
123 124 2.276740 CCAAGGTGGATCCCAGGC 59.723 66.667 9.90 0.00 40.96 4.85
124 125 2.276740 CAAGGTGGATCCCAGGCC 59.723 66.667 9.90 6.47 32.34 5.19
125 126 3.023735 AAGGTGGATCCCAGGCCC 61.024 66.667 9.90 1.34 32.34 5.80
145 146 4.980805 GGTTGCACCAGCCGTCGA 62.981 66.667 0.00 0.00 38.42 4.20
146 147 3.414700 GTTGCACCAGCCGTCGAG 61.415 66.667 0.00 0.00 41.13 4.04
147 148 4.680237 TTGCACCAGCCGTCGAGG 62.680 66.667 0.00 0.00 41.13 4.63
185 186 4.489771 GCCCCACCACCTCCGATG 62.490 72.222 0.00 0.00 0.00 3.84
186 187 4.489771 CCCCACCACCTCCGATGC 62.490 72.222 0.00 0.00 0.00 3.91
187 188 4.489771 CCCACCACCTCCGATGCC 62.490 72.222 0.00 0.00 0.00 4.40
188 189 4.838152 CCACCACCTCCGATGCCG 62.838 72.222 0.00 0.00 0.00 5.69
189 190 3.770040 CACCACCTCCGATGCCGA 61.770 66.667 0.00 0.00 38.22 5.54
190 191 3.461773 ACCACCTCCGATGCCGAG 61.462 66.667 0.00 0.00 38.22 4.63
191 192 4.899239 CCACCTCCGATGCCGAGC 62.899 72.222 0.00 0.00 38.22 5.03
192 193 4.147449 CACCTCCGATGCCGAGCA 62.147 66.667 1.01 1.01 44.86 4.26
193 194 3.842923 ACCTCCGATGCCGAGCAG 61.843 66.667 4.90 0.00 43.65 4.24
194 195 4.598894 CCTCCGATGCCGAGCAGG 62.599 72.222 4.90 2.14 43.65 4.85
195 196 4.598894 CTCCGATGCCGAGCAGGG 62.599 72.222 4.90 8.12 43.65 4.45
197 198 4.899239 CCGATGCCGAGCAGGGAC 62.899 72.222 11.02 1.36 45.60 4.46
233 234 4.101790 CGCCACACCGCCAATGTC 62.102 66.667 0.00 0.00 0.00 3.06
234 235 2.983030 GCCACACCGCCAATGTCA 60.983 61.111 0.00 0.00 0.00 3.58
235 236 2.953821 CCACACCGCCAATGTCAC 59.046 61.111 0.00 0.00 0.00 3.67
236 237 2.625823 CCACACCGCCAATGTCACC 61.626 63.158 0.00 0.00 0.00 4.02
237 238 2.668212 ACACCGCCAATGTCACCG 60.668 61.111 0.00 0.00 0.00 4.94
238 239 3.430862 CACCGCCAATGTCACCGG 61.431 66.667 0.00 0.00 45.80 5.28
257 258 4.593864 GGCCAGATCCGAGCCGTC 62.594 72.222 0.00 0.00 36.84 4.79
258 259 4.933064 GCCAGATCCGAGCCGTCG 62.933 72.222 0.00 0.00 46.39 5.12
259 260 3.518998 CCAGATCCGAGCCGTCGT 61.519 66.667 0.00 0.00 45.30 4.34
260 261 2.490217 CAGATCCGAGCCGTCGTT 59.510 61.111 0.00 0.00 45.30 3.85
261 262 1.874019 CAGATCCGAGCCGTCGTTG 60.874 63.158 0.00 0.00 45.30 4.10
262 263 2.582498 GATCCGAGCCGTCGTTGG 60.582 66.667 0.00 0.00 45.30 3.77
263 264 4.143333 ATCCGAGCCGTCGTTGGG 62.143 66.667 0.00 0.00 45.30 4.12
294 295 4.760047 GGAGCTGCGCCGGAAAGA 62.760 66.667 5.05 0.00 0.00 2.52
295 296 2.512515 GAGCTGCGCCGGAAAGAT 60.513 61.111 5.05 0.00 0.00 2.40
296 297 2.817423 GAGCTGCGCCGGAAAGATG 61.817 63.158 5.05 0.00 0.00 2.90
297 298 4.543084 GCTGCGCCGGAAAGATGC 62.543 66.667 5.05 0.00 0.00 3.91
298 299 3.880846 CTGCGCCGGAAAGATGCC 61.881 66.667 5.05 0.00 0.00 4.40
326 327 4.047059 CGCACTGCCAGGGCTTTG 62.047 66.667 18.25 9.32 44.04 2.77
327 328 4.368543 GCACTGCCAGGGCTTTGC 62.369 66.667 12.78 17.09 42.59 3.68
357 358 4.394078 CACGACGTCGGCGAGGAA 62.394 66.667 37.89 0.00 44.95 3.36
358 359 4.099170 ACGACGTCGGCGAGGAAG 62.099 66.667 37.89 25.69 44.95 3.46
359 360 4.831307 CGACGTCGGCGAGGAAGG 62.831 72.222 32.97 17.96 42.00 3.46
360 361 4.493747 GACGTCGGCGAGGAAGGG 62.494 72.222 32.97 10.89 42.00 3.95
362 363 4.194720 CGTCGGCGAGGAAGGGAG 62.195 72.222 23.88 0.00 41.33 4.30
363 364 3.839432 GTCGGCGAGGAAGGGAGG 61.839 72.222 11.20 0.00 0.00 4.30
369 370 4.798682 GAGGAAGGGAGGCGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
370 371 4.348495 AGGAAGGGAGGCGGGGAA 62.348 66.667 0.00 0.00 0.00 3.97
371 372 3.798511 GGAAGGGAGGCGGGGAAG 61.799 72.222 0.00 0.00 0.00 3.46
372 373 3.798511 GAAGGGAGGCGGGGAAGG 61.799 72.222 0.00 0.00 0.00 3.46
373 374 4.348495 AAGGGAGGCGGGGAAGGA 62.348 66.667 0.00 0.00 0.00 3.36
374 375 4.806339 AGGGAGGCGGGGAAGGAG 62.806 72.222 0.00 0.00 0.00 3.69
400 401 3.547513 GGCGAGGCGGATAGGGTT 61.548 66.667 0.00 0.00 0.00 4.11
401 402 2.029221 GCGAGGCGGATAGGGTTC 59.971 66.667 0.00 0.00 0.00 3.62
402 403 2.735237 CGAGGCGGATAGGGTTCC 59.265 66.667 0.00 0.00 0.00 3.62
403 404 2.868986 CGAGGCGGATAGGGTTCCC 61.869 68.421 0.00 0.00 31.61 3.97
404 405 2.447959 AGGCGGATAGGGTTCCCC 60.448 66.667 4.02 0.00 45.90 4.81
414 415 4.280019 GGTTCCCCCGTGTTGCCT 62.280 66.667 0.00 0.00 0.00 4.75
415 416 2.203437 GTTCCCCCGTGTTGCCTT 60.203 61.111 0.00 0.00 0.00 4.35
416 417 1.073548 GTTCCCCCGTGTTGCCTTA 59.926 57.895 0.00 0.00 0.00 2.69
417 418 0.958876 GTTCCCCCGTGTTGCCTTAG 60.959 60.000 0.00 0.00 0.00 2.18
418 419 1.128809 TTCCCCCGTGTTGCCTTAGA 61.129 55.000 0.00 0.00 0.00 2.10
419 420 1.078426 CCCCCGTGTTGCCTTAGAG 60.078 63.158 0.00 0.00 0.00 2.43
420 421 1.550130 CCCCCGTGTTGCCTTAGAGA 61.550 60.000 0.00 0.00 0.00 3.10
421 422 0.108138 CCCCGTGTTGCCTTAGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
423 424 0.108138 CCGTGTTGCCTTAGAGAGGG 60.108 60.000 0.00 0.00 46.40 4.30
424 425 0.895530 CGTGTTGCCTTAGAGAGGGA 59.104 55.000 0.00 0.00 46.40 4.20
425 426 1.404315 CGTGTTGCCTTAGAGAGGGAC 60.404 57.143 0.00 0.00 46.74 4.46
426 427 0.895530 TGTTGCCTTAGAGAGGGACG 59.104 55.000 0.00 0.00 46.74 4.79
427 428 0.460459 GTTGCCTTAGAGAGGGACGC 60.460 60.000 0.00 0.00 46.74 5.19
428 429 1.945354 TTGCCTTAGAGAGGGACGCG 61.945 60.000 3.53 3.53 46.74 6.01
429 430 3.121019 CCTTAGAGAGGGACGCGG 58.879 66.667 12.47 0.00 42.26 6.46
430 431 2.491022 CCTTAGAGAGGGACGCGGG 61.491 68.421 12.47 0.00 42.26 6.13
431 432 2.441532 TTAGAGAGGGACGCGGGG 60.442 66.667 12.47 0.00 0.00 5.73
432 433 4.517934 TAGAGAGGGACGCGGGGG 62.518 72.222 12.47 0.00 0.00 5.40
443 444 3.151022 GCGGGGGTCAGGAGAGAG 61.151 72.222 0.00 0.00 0.00 3.20
444 445 2.443016 CGGGGGTCAGGAGAGAGG 60.443 72.222 0.00 0.00 0.00 3.69
445 446 2.997584 CGGGGGTCAGGAGAGAGGA 61.998 68.421 0.00 0.00 0.00 3.71
446 447 1.629297 GGGGGTCAGGAGAGAGGAT 59.371 63.158 0.00 0.00 0.00 3.24
447 448 0.030603 GGGGGTCAGGAGAGAGGATT 60.031 60.000 0.00 0.00 0.00 3.01
448 449 1.220750 GGGGGTCAGGAGAGAGGATTA 59.779 57.143 0.00 0.00 0.00 1.75
449 450 2.158081 GGGGGTCAGGAGAGAGGATTAT 60.158 54.545 0.00 0.00 0.00 1.28
450 451 3.077695 GGGGGTCAGGAGAGAGGATTATA 59.922 52.174 0.00 0.00 0.00 0.98
451 452 4.349365 GGGGTCAGGAGAGAGGATTATAG 58.651 52.174 0.00 0.00 0.00 1.31
452 453 4.202738 GGGGTCAGGAGAGAGGATTATAGT 60.203 50.000 0.00 0.00 0.00 2.12
453 454 5.399113 GGGTCAGGAGAGAGGATTATAGTT 58.601 45.833 0.00 0.00 0.00 2.24
454 455 6.468945 GGGGTCAGGAGAGAGGATTATAGTTA 60.469 46.154 0.00 0.00 0.00 2.24
455 456 6.661805 GGGTCAGGAGAGAGGATTATAGTTAG 59.338 46.154 0.00 0.00 0.00 2.34
456 457 6.661805 GGTCAGGAGAGAGGATTATAGTTAGG 59.338 46.154 0.00 0.00 0.00 2.69
457 458 7.463431 GTCAGGAGAGAGGATTATAGTTAGGA 58.537 42.308 0.00 0.00 0.00 2.94
458 459 7.945664 GTCAGGAGAGAGGATTATAGTTAGGAA 59.054 40.741 0.00 0.00 0.00 3.36
459 460 8.511969 TCAGGAGAGAGGATTATAGTTAGGAAA 58.488 37.037 0.00 0.00 0.00 3.13
460 461 9.148879 CAGGAGAGAGGATTATAGTTAGGAAAA 57.851 37.037 0.00 0.00 0.00 2.29
461 462 9.906274 AGGAGAGAGGATTATAGTTAGGAAAAT 57.094 33.333 0.00 0.00 0.00 1.82
486 487 5.182525 CGTTACTTTACGTAGCCTTGTTC 57.817 43.478 0.00 0.00 36.80 3.18
487 488 4.201428 CGTTACTTTACGTAGCCTTGTTCG 60.201 45.833 0.00 0.00 36.80 3.95
488 489 3.375782 ACTTTACGTAGCCTTGTTCGT 57.624 42.857 0.00 0.00 39.74 3.85
489 490 4.503741 ACTTTACGTAGCCTTGTTCGTA 57.496 40.909 0.00 0.00 37.66 3.43
490 491 4.479619 ACTTTACGTAGCCTTGTTCGTAG 58.520 43.478 0.00 0.00 39.33 3.51
491 492 4.216257 ACTTTACGTAGCCTTGTTCGTAGA 59.784 41.667 0.00 0.00 39.33 2.59
492 493 4.970662 TTACGTAGCCTTGTTCGTAGAT 57.029 40.909 0.00 0.00 39.33 1.98
493 494 3.146618 ACGTAGCCTTGTTCGTAGATG 57.853 47.619 0.00 0.00 35.04 2.90
494 495 2.159282 ACGTAGCCTTGTTCGTAGATGG 60.159 50.000 0.00 0.00 35.04 3.51
495 496 2.098607 CGTAGCCTTGTTCGTAGATGGA 59.901 50.000 0.00 0.00 35.04 3.41
496 497 2.969628 AGCCTTGTTCGTAGATGGAG 57.030 50.000 0.00 0.00 35.04 3.86
497 498 1.134670 AGCCTTGTTCGTAGATGGAGC 60.135 52.381 0.00 0.00 35.04 4.70
498 499 1.405526 GCCTTGTTCGTAGATGGAGCA 60.406 52.381 0.00 0.00 35.04 4.26
499 500 2.743183 GCCTTGTTCGTAGATGGAGCAT 60.743 50.000 0.00 0.00 35.04 3.79
500 501 3.535561 CCTTGTTCGTAGATGGAGCATT 58.464 45.455 0.00 0.00 35.04 3.56
501 502 4.693283 CCTTGTTCGTAGATGGAGCATTA 58.307 43.478 0.00 0.00 35.04 1.90
502 503 5.300752 CCTTGTTCGTAGATGGAGCATTAT 58.699 41.667 0.00 0.00 35.04 1.28
503 504 5.406780 CCTTGTTCGTAGATGGAGCATTATC 59.593 44.000 0.00 0.00 35.04 1.75
504 505 4.546570 TGTTCGTAGATGGAGCATTATCG 58.453 43.478 0.00 0.00 35.04 2.92
505 506 4.037565 TGTTCGTAGATGGAGCATTATCGT 59.962 41.667 0.00 0.00 35.04 3.73
506 507 4.848562 TCGTAGATGGAGCATTATCGTT 57.151 40.909 0.00 0.00 0.00 3.85
507 508 5.196341 TCGTAGATGGAGCATTATCGTTT 57.804 39.130 0.00 0.00 0.00 3.60
508 509 6.321848 TCGTAGATGGAGCATTATCGTTTA 57.678 37.500 0.00 0.00 0.00 2.01
509 510 6.379386 TCGTAGATGGAGCATTATCGTTTAG 58.621 40.000 0.00 0.00 0.00 1.85
510 511 5.573282 CGTAGATGGAGCATTATCGTTTAGG 59.427 44.000 0.00 0.00 0.00 2.69
511 512 5.808366 AGATGGAGCATTATCGTTTAGGA 57.192 39.130 0.00 0.00 0.00 2.94
512 513 6.174720 AGATGGAGCATTATCGTTTAGGAA 57.825 37.500 0.00 0.00 0.00 3.36
513 514 6.773638 AGATGGAGCATTATCGTTTAGGAAT 58.226 36.000 0.00 0.00 0.00 3.01
514 515 7.907389 AGATGGAGCATTATCGTTTAGGAATA 58.093 34.615 0.00 0.00 0.00 1.75
515 516 8.037758 AGATGGAGCATTATCGTTTAGGAATAG 58.962 37.037 0.00 0.00 0.00 1.73
516 517 7.297936 TGGAGCATTATCGTTTAGGAATAGA 57.702 36.000 0.00 0.00 0.00 1.98
517 518 7.378966 TGGAGCATTATCGTTTAGGAATAGAG 58.621 38.462 0.00 0.00 0.00 2.43
518 519 7.015292 TGGAGCATTATCGTTTAGGAATAGAGT 59.985 37.037 0.00 0.00 0.00 3.24
519 520 8.521176 GGAGCATTATCGTTTAGGAATAGAGTA 58.479 37.037 0.00 0.00 0.00 2.59
521 522 9.862371 AGCATTATCGTTTAGGAATAGAGTATG 57.138 33.333 0.00 0.00 0.00 2.39
522 523 9.088512 GCATTATCGTTTAGGAATAGAGTATGG 57.911 37.037 0.00 0.00 0.00 2.74
525 526 9.584008 TTATCGTTTAGGAATAGAGTATGGAGT 57.416 33.333 0.00 0.00 0.00 3.85
527 528 8.618702 TCGTTTAGGAATAGAGTATGGAGTAG 57.381 38.462 0.00 0.00 0.00 2.57
528 529 8.435187 TCGTTTAGGAATAGAGTATGGAGTAGA 58.565 37.037 0.00 0.00 0.00 2.59
529 530 9.233649 CGTTTAGGAATAGAGTATGGAGTAGAT 57.766 37.037 0.00 0.00 0.00 1.98
539 540 8.415950 AGAGTATGGAGTAGATGATTAACCAG 57.584 38.462 0.00 0.00 0.00 4.00
540 541 8.007742 AGAGTATGGAGTAGATGATTAACCAGT 58.992 37.037 0.00 0.00 0.00 4.00
541 542 7.957002 AGTATGGAGTAGATGATTAACCAGTG 58.043 38.462 0.00 0.00 0.00 3.66
542 543 7.785028 AGTATGGAGTAGATGATTAACCAGTGA 59.215 37.037 0.00 0.00 0.00 3.41
543 544 7.623999 ATGGAGTAGATGATTAACCAGTGAT 57.376 36.000 0.00 0.00 0.00 3.06
567 568 2.875087 TTTTCGGAGTCTGTCGACAA 57.125 45.000 20.49 7.97 42.73 3.18
568 569 2.129823 TTTCGGAGTCTGTCGACAAC 57.870 50.000 20.49 18.75 42.73 3.32
569 570 1.315690 TTCGGAGTCTGTCGACAACT 58.684 50.000 24.04 24.04 42.73 3.16
576 577 5.176958 CGGAGTCTGTCGACAACTAATTTTT 59.823 40.000 23.92 8.79 42.73 1.94
577 578 6.363473 GGAGTCTGTCGACAACTAATTTTTG 58.637 40.000 23.92 9.68 42.73 2.44
702 706 1.420138 ACTCCGAAACATCACACCCTT 59.580 47.619 0.00 0.00 0.00 3.95
705 709 4.261801 CTCCGAAACATCACACCCTTAAT 58.738 43.478 0.00 0.00 0.00 1.40
716 720 6.306643 TCACACCCTTAATATGTCATGTGA 57.693 37.500 0.00 0.00 42.03 3.58
726 730 2.103042 GTCATGTGAGCTCACCGCC 61.103 63.158 37.23 21.57 45.88 6.13
792 797 2.040544 CGGTGGCTAGGCAAACCAG 61.041 63.158 22.04 11.13 36.87 4.00
843 848 4.115199 CCACTGCTACTGGGCCCC 62.115 72.222 22.27 3.07 0.00 5.80
1142 1154 1.753368 GCATTCCTCCTCTCCTCCGG 61.753 65.000 0.00 0.00 0.00 5.14
1812 1830 1.078426 GTACCTGCCTGCATTCCGT 60.078 57.895 0.00 0.00 0.00 4.69
1880 1898 0.106619 ATCGCCTACTCCGACTTCCT 60.107 55.000 0.00 0.00 37.56 3.36
1887 1905 0.969894 ACTCCGACTTCCTGTTCCTG 59.030 55.000 0.00 0.00 0.00 3.86
1898 1916 1.611673 CCTGTTCCTGAACGCCTCATT 60.612 52.381 5.62 0.00 43.94 2.57
1971 1995 5.278561 GGTCGATTACCTGAGATTCTACCTG 60.279 48.000 0.00 0.00 45.75 4.00
2040 2064 2.107378 TGTGGTGGTGCAGAAGGATTTA 59.893 45.455 0.00 0.00 0.00 1.40
2076 2100 1.003233 GTCGACTTGGATGGGAAGGTT 59.997 52.381 8.70 0.00 0.00 3.50
2151 2175 1.191535 ACTTCACGCAGGCCATAGTA 58.808 50.000 5.01 0.00 0.00 1.82
2293 2331 4.046938 TGCGGCAATCTTTTGTTACAAA 57.953 36.364 6.41 6.41 35.17 2.83
2449 2487 8.184192 ACTTAAGTTTCTTTGTCACTGTCATTG 58.816 33.333 1.12 0.00 0.00 2.82
2552 2604 6.183360 TGGTAAAATGTTTTGGAAGGAACTCC 60.183 38.462 1.16 0.00 38.49 3.85
2575 2627 4.479158 TGGGAAACAACTCCATTAAGCTT 58.521 39.130 3.48 3.48 37.20 3.74
2688 2740 4.976116 GGCTGTAATGTTTCACAACTCAAC 59.024 41.667 0.00 0.00 33.58 3.18
2717 2769 5.519206 CCGCAAGTTAGTACTTTACCATCTC 59.481 44.000 0.00 0.00 41.85 2.75
2938 2990 9.984190 TCTTCTCTTTGAGAATCTCATGATATG 57.016 33.333 14.31 10.00 45.84 1.78
2939 2991 9.210329 CTTCTCTTTGAGAATCTCATGATATGG 57.790 37.037 14.31 4.59 45.84 2.74
2940 2992 8.260099 TCTCTTTGAGAATCTCATGATATGGT 57.740 34.615 14.31 0.00 40.39 3.55
2941 2993 9.372189 TCTCTTTGAGAATCTCATGATATGGTA 57.628 33.333 14.31 0.00 40.39 3.25
2942 2994 9.421806 CTCTTTGAGAATCTCATGATATGGTAC 57.578 37.037 14.31 0.00 40.39 3.34
2945 2997 9.770097 TTTGAGAATCTCATGATATGGTACTTC 57.230 33.333 14.31 0.00 40.39 3.01
2947 2999 9.152327 TGAGAATCTCATGATATGGTACTTCTT 57.848 33.333 9.18 0.00 35.39 2.52
2981 3033 9.654919 AATACCTAAATATGTGCCATTACCTTT 57.345 29.630 0.00 0.00 0.00 3.11
2984 3036 8.474831 ACCTAAATATGTGCCATTACCTTTTTC 58.525 33.333 0.00 0.00 0.00 2.29
2993 3045 6.863645 GTGCCATTACCTTTTTCTTCTTCTTC 59.136 38.462 0.00 0.00 0.00 2.87
3119 3179 4.686091 TGACTGTCGACTTCATGACAATTC 59.314 41.667 17.92 0.00 43.91 2.17
3237 3297 9.561069 CCAAATCTACAACCACTAAGCTAATAT 57.439 33.333 0.00 0.00 0.00 1.28
3406 3466 3.058224 GTGTACCTCACCAAAGCATTGAC 60.058 47.826 2.61 0.00 40.84 3.18
3579 3640 0.911045 TCCAAGCATCAGCCCTGAGA 60.911 55.000 4.16 0.00 43.61 3.27
3608 3669 1.734465 GGTGCTGCAGTGATACACTTC 59.266 52.381 16.64 0.00 42.59 3.01
4004 4084 6.543831 CCAACTGTATTTATGGAAAGGAGGAG 59.456 42.308 0.00 0.00 34.82 3.69
4069 4152 6.801575 TGTCACCTTCTTATTTTGTTTCACC 58.198 36.000 0.00 0.00 0.00 4.02
4136 4219 2.095059 GCCATGTTGTGAGCGAAATTCT 60.095 45.455 0.00 0.00 0.00 2.40
4147 4230 3.873952 GAGCGAAATTCTGTAGATTGGCT 59.126 43.478 4.96 4.96 0.00 4.75
4162 4245 4.710375 AGATTGGCTCTTCATCAGCAATTT 59.290 37.500 0.00 0.00 38.77 1.82
4171 4254 7.697291 GCTCTTCATCAGCAATTTCTTCTAAAG 59.303 37.037 0.00 0.00 36.82 1.85
4334 4417 6.378582 TGCTTTTCTTCCACGTATTTGATTC 58.621 36.000 0.00 0.00 0.00 2.52
4347 4430 4.844349 ATTTGATTCTCTTCCCCTCGAA 57.156 40.909 0.00 0.00 0.00 3.71
4348 4431 3.611766 TTGATTCTCTTCCCCTCGAAC 57.388 47.619 0.00 0.00 0.00 3.95
4374 4457 9.798994 CGACTAAATACTTTGGTACTTATCACT 57.201 33.333 0.00 0.00 34.29 3.41
4438 4530 6.395426 TTTATTATCTCCATTGCTTGCTGG 57.605 37.500 0.00 0.00 0.00 4.85
4578 4670 7.330700 CCTTGAGCAAGTTTCTTCTTCTAGTAG 59.669 40.741 9.18 0.00 36.72 2.57
4579 4671 7.526142 TGAGCAAGTTTCTTCTTCTAGTAGA 57.474 36.000 0.00 0.00 0.00 2.59
4598 4690 6.556639 AGTAGATATCTATGAGCAGGTTGGA 58.443 40.000 15.43 0.00 0.00 3.53
4671 4763 1.962807 TCCAAGAATGCCCACAACTTG 59.037 47.619 0.00 0.00 40.61 3.16
4719 4812 2.202987 GGGCGAGTGAGCAGATGG 60.203 66.667 0.00 0.00 39.27 3.51
4729 4822 2.027745 GTGAGCAGATGGAGAAACAGGA 60.028 50.000 0.00 0.00 0.00 3.86
4730 4823 2.639347 TGAGCAGATGGAGAAACAGGAA 59.361 45.455 0.00 0.00 0.00 3.36
4802 4897 9.897744 GACTTGACAGAACATCATCAAAAATAA 57.102 29.630 0.00 0.00 31.00 1.40
4843 4938 7.043059 GGCACAATTCGTTGAATGAAGTAAAAA 60.043 33.333 5.99 0.00 32.14 1.94
4875 4970 5.607939 AATCCGTTAAATGGGGAAATTCC 57.392 39.130 2.79 2.79 35.23 3.01
4900 4995 7.982354 CCTGTTAAAACATGTAAAAACAAGGGA 59.018 33.333 16.12 0.41 38.41 4.20
5026 5122 1.078709 CTCTGTATGCCGTGTTGGTG 58.921 55.000 0.00 0.00 41.21 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.715523 TGGTGGTTGGCTAGCGGC 62.716 66.667 9.00 0.79 40.90 6.53
3 4 2.746277 GTGGTGGTTGGCTAGCGG 60.746 66.667 9.00 0.00 0.00 5.52
4 5 2.746277 GGTGGTGGTTGGCTAGCG 60.746 66.667 9.00 0.00 0.00 4.26
6 7 2.046314 CCGGTGGTGGTTGGCTAG 60.046 66.667 0.00 0.00 0.00 3.42
7 8 3.642503 CCCGGTGGTGGTTGGCTA 61.643 66.667 0.00 0.00 0.00 3.93
15 16 4.436998 GACTCGCTCCCGGTGGTG 62.437 72.222 0.00 0.00 34.56 4.17
27 28 4.426112 TGGCTCTGCTGCGACTCG 62.426 66.667 0.00 0.00 0.00 4.18
28 29 2.813042 GTGGCTCTGCTGCGACTC 60.813 66.667 0.00 0.00 38.38 3.36
29 30 4.731612 CGTGGCTCTGCTGCGACT 62.732 66.667 0.00 0.00 39.08 4.18
33 34 4.704833 TTCCCGTGGCTCTGCTGC 62.705 66.667 0.00 0.00 0.00 5.25
34 35 2.743928 GTTCCCGTGGCTCTGCTG 60.744 66.667 0.00 0.00 0.00 4.41
35 36 3.241530 TGTTCCCGTGGCTCTGCT 61.242 61.111 0.00 0.00 0.00 4.24
36 37 3.050275 GTGTTCCCGTGGCTCTGC 61.050 66.667 0.00 0.00 0.00 4.26
37 38 2.358737 GGTGTTCCCGTGGCTCTG 60.359 66.667 0.00 0.00 0.00 3.35
38 39 2.847234 TGGTGTTCCCGTGGCTCT 60.847 61.111 0.00 0.00 35.15 4.09
39 40 2.668550 GTGGTGTTCCCGTGGCTC 60.669 66.667 0.00 0.00 35.15 4.70
40 41 3.168528 AGTGGTGTTCCCGTGGCT 61.169 61.111 0.00 0.00 35.15 4.75
41 42 2.668550 GAGTGGTGTTCCCGTGGC 60.669 66.667 0.00 0.00 35.15 5.01
42 43 2.032071 GGAGTGGTGTTCCCGTGG 59.968 66.667 0.00 0.00 35.15 4.94
43 44 0.955428 CATGGAGTGGTGTTCCCGTG 60.955 60.000 0.00 0.00 35.15 4.94
44 45 1.374947 CATGGAGTGGTGTTCCCGT 59.625 57.895 0.00 0.00 35.15 5.28
45 46 2.040544 GCATGGAGTGGTGTTCCCG 61.041 63.158 0.00 0.00 35.15 5.14
46 47 1.678970 GGCATGGAGTGGTGTTCCC 60.679 63.158 0.00 0.00 33.62 3.97
47 48 0.618458 TAGGCATGGAGTGGTGTTCC 59.382 55.000 0.00 0.00 35.20 3.62
48 49 2.084546 GTTAGGCATGGAGTGGTGTTC 58.915 52.381 0.00 0.00 0.00 3.18
49 50 1.423541 TGTTAGGCATGGAGTGGTGTT 59.576 47.619 0.00 0.00 0.00 3.32
50 51 1.003580 CTGTTAGGCATGGAGTGGTGT 59.996 52.381 0.00 0.00 0.00 4.16
51 52 1.278985 TCTGTTAGGCATGGAGTGGTG 59.721 52.381 0.00 0.00 0.00 4.17
52 53 1.556911 CTCTGTTAGGCATGGAGTGGT 59.443 52.381 0.00 0.00 0.00 4.16
53 54 1.134280 CCTCTGTTAGGCATGGAGTGG 60.134 57.143 0.00 0.00 38.97 4.00
54 55 2.322355 CCTCTGTTAGGCATGGAGTG 57.678 55.000 0.00 0.00 38.97 3.51
64 65 1.337823 CGGGGTTGTGACCTCTGTTAG 60.338 57.143 0.00 0.00 44.88 2.34
65 66 0.682852 CGGGGTTGTGACCTCTGTTA 59.317 55.000 0.00 0.00 44.88 2.41
66 67 1.052124 TCGGGGTTGTGACCTCTGTT 61.052 55.000 0.00 0.00 44.88 3.16
67 68 1.052124 TTCGGGGTTGTGACCTCTGT 61.052 55.000 0.00 0.00 44.88 3.41
68 69 0.602905 GTTCGGGGTTGTGACCTCTG 60.603 60.000 0.00 0.00 44.88 3.35
69 70 1.752833 GTTCGGGGTTGTGACCTCT 59.247 57.895 0.00 0.00 44.88 3.69
70 71 1.302271 GGTTCGGGGTTGTGACCTC 60.302 63.158 0.00 0.00 45.75 3.85
71 72 2.826003 GGGTTCGGGGTTGTGACCT 61.826 63.158 0.00 0.00 45.75 3.85
72 73 2.281970 GGGTTCGGGGTTGTGACC 60.282 66.667 0.00 0.00 45.75 4.02
73 74 2.281970 GGGGTTCGGGGTTGTGAC 60.282 66.667 0.00 0.00 0.00 3.67
74 75 3.943691 CGGGGTTCGGGGTTGTGA 61.944 66.667 0.00 0.00 34.75 3.58
92 93 4.113815 TTGGCTGGATCTGGGCGG 62.114 66.667 0.00 0.00 0.00 6.13
93 94 2.515523 CTTGGCTGGATCTGGGCG 60.516 66.667 0.00 0.00 0.00 6.13
94 95 2.123982 CCTTGGCTGGATCTGGGC 60.124 66.667 0.00 0.00 0.00 5.36
95 96 1.077212 CACCTTGGCTGGATCTGGG 60.077 63.158 4.24 0.00 0.00 4.45
96 97 1.077212 CCACCTTGGCTGGATCTGG 60.077 63.158 4.24 0.00 0.00 3.86
97 98 0.549950 ATCCACCTTGGCTGGATCTG 59.450 55.000 13.98 0.00 43.94 2.90
98 99 3.033746 ATCCACCTTGGCTGGATCT 57.966 52.632 13.98 0.78 43.94 2.75
101 102 2.308722 GGGATCCACCTTGGCTGGA 61.309 63.158 15.23 11.40 42.17 3.86
102 103 2.276740 GGGATCCACCTTGGCTGG 59.723 66.667 15.23 3.06 37.47 4.85
103 104 1.077212 CTGGGATCCACCTTGGCTG 60.077 63.158 15.23 0.00 37.47 4.85
104 105 2.311854 CCTGGGATCCACCTTGGCT 61.312 63.158 15.23 0.00 37.47 4.75
105 106 2.276740 CCTGGGATCCACCTTGGC 59.723 66.667 15.23 0.00 37.47 4.52
106 107 2.276740 GCCTGGGATCCACCTTGG 59.723 66.667 15.23 8.55 39.43 3.61
107 108 2.276740 GGCCTGGGATCCACCTTG 59.723 66.667 15.23 0.00 38.98 3.61
108 109 3.023735 GGGCCTGGGATCCACCTT 61.024 66.667 15.23 0.00 38.98 3.50
129 130 3.414700 CTCGACGGCTGGTGCAAC 61.415 66.667 0.00 0.00 41.91 4.17
130 131 4.680237 CCTCGACGGCTGGTGCAA 62.680 66.667 0.00 0.00 41.91 4.08
168 169 4.489771 CATCGGAGGTGGTGGGGC 62.490 72.222 0.00 0.00 0.00 5.80
169 170 4.489771 GCATCGGAGGTGGTGGGG 62.490 72.222 0.00 0.00 0.00 4.96
170 171 4.489771 GGCATCGGAGGTGGTGGG 62.490 72.222 0.00 0.00 0.00 4.61
171 172 4.838152 CGGCATCGGAGGTGGTGG 62.838 72.222 0.00 0.00 0.00 4.61
172 173 3.723235 CTCGGCATCGGAGGTGGTG 62.723 68.421 0.00 0.00 36.95 4.17
173 174 3.461773 CTCGGCATCGGAGGTGGT 61.462 66.667 0.00 0.00 36.95 4.16
174 175 4.899239 GCTCGGCATCGGAGGTGG 62.899 72.222 4.06 0.00 36.95 4.61
175 176 4.147449 TGCTCGGCATCGGAGGTG 62.147 66.667 4.06 0.00 36.95 4.00
176 177 3.842923 CTGCTCGGCATCGGAGGT 61.843 66.667 0.00 0.00 38.13 3.85
177 178 4.598894 CCTGCTCGGCATCGGAGG 62.599 72.222 0.00 0.00 38.13 4.30
178 179 4.598894 CCCTGCTCGGCATCGGAG 62.599 72.222 0.00 0.00 38.13 4.63
180 181 4.899239 GTCCCTGCTCGGCATCGG 62.899 72.222 0.00 3.17 38.13 4.18
193 194 4.736896 GAGACACGGTGGCGTCCC 62.737 72.222 13.48 0.00 32.33 4.46
194 195 4.736896 GGAGACACGGTGGCGTCC 62.737 72.222 13.48 13.84 32.33 4.79
217 218 2.983030 TGACATTGGCGGTGTGGC 60.983 61.111 0.00 0.00 45.12 5.01
218 219 2.625823 GGTGACATTGGCGGTGTGG 61.626 63.158 0.00 0.00 0.00 4.17
219 220 2.953821 GGTGACATTGGCGGTGTG 59.046 61.111 0.00 0.00 0.00 3.82
220 221 2.668212 CGGTGACATTGGCGGTGT 60.668 61.111 0.00 0.00 0.00 4.16
221 222 3.430862 CCGGTGACATTGGCGGTG 61.431 66.667 0.00 0.00 0.00 4.94
240 241 4.593864 GACGGCTCGGATCTGGCC 62.594 72.222 18.98 18.98 42.18 5.36
241 242 4.933064 CGACGGCTCGGATCTGGC 62.933 72.222 0.62 4.13 36.16 4.85
242 243 3.064987 AACGACGGCTCGGATCTGG 62.065 63.158 0.62 0.00 44.80 3.86
243 244 1.874019 CAACGACGGCTCGGATCTG 60.874 63.158 0.00 0.00 44.80 2.90
244 245 2.490217 CAACGACGGCTCGGATCT 59.510 61.111 0.00 0.00 44.80 2.75
245 246 2.582498 CCAACGACGGCTCGGATC 60.582 66.667 0.00 0.00 44.80 3.36
246 247 4.143333 CCCAACGACGGCTCGGAT 62.143 66.667 0.00 0.00 44.80 4.18
281 282 3.880846 GGCATCTTTCCGGCGCAG 61.881 66.667 10.83 4.65 0.00 5.18
309 310 4.047059 CAAAGCCCTGGCAGTGCG 62.047 66.667 16.22 2.82 44.88 5.34
310 311 4.368543 GCAAAGCCCTGGCAGTGC 62.369 66.667 14.46 14.46 44.88 4.40
311 312 3.688159 GGCAAAGCCCTGGCAGTG 61.688 66.667 14.43 2.47 44.06 3.66
340 341 4.394078 TTCCTCGCCGACGTCGTG 62.394 66.667 33.49 25.44 41.18 4.35
341 342 4.099170 CTTCCTCGCCGACGTCGT 62.099 66.667 33.49 0.00 41.18 4.34
342 343 4.831307 CCTTCCTCGCCGACGTCG 62.831 72.222 30.33 30.33 41.18 5.12
343 344 4.493747 CCCTTCCTCGCCGACGTC 62.494 72.222 5.18 5.18 41.18 4.34
345 346 4.194720 CTCCCTTCCTCGCCGACG 62.195 72.222 0.00 0.00 42.01 5.12
346 347 3.839432 CCTCCCTTCCTCGCCGAC 61.839 72.222 0.00 0.00 0.00 4.79
352 353 4.798682 TCCCCGCCTCCCTTCCTC 62.799 72.222 0.00 0.00 0.00 3.71
353 354 4.348495 TTCCCCGCCTCCCTTCCT 62.348 66.667 0.00 0.00 0.00 3.36
354 355 3.798511 CTTCCCCGCCTCCCTTCC 61.799 72.222 0.00 0.00 0.00 3.46
355 356 3.798511 CCTTCCCCGCCTCCCTTC 61.799 72.222 0.00 0.00 0.00 3.46
356 357 4.348495 TCCTTCCCCGCCTCCCTT 62.348 66.667 0.00 0.00 0.00 3.95
357 358 4.806339 CTCCTTCCCCGCCTCCCT 62.806 72.222 0.00 0.00 0.00 4.20
383 384 3.516866 GAACCCTATCCGCCTCGCC 62.517 68.421 0.00 0.00 0.00 5.54
384 385 2.029221 GAACCCTATCCGCCTCGC 59.971 66.667 0.00 0.00 0.00 5.03
385 386 2.735237 GGAACCCTATCCGCCTCG 59.265 66.667 0.00 0.00 0.00 4.63
398 399 0.958876 CTAAGGCAACACGGGGGAAC 60.959 60.000 0.00 0.00 41.41 3.62
399 400 1.128809 TCTAAGGCAACACGGGGGAA 61.129 55.000 0.00 0.00 41.41 3.97
400 401 1.536907 TCTAAGGCAACACGGGGGA 60.537 57.895 0.00 0.00 41.41 4.81
401 402 1.078426 CTCTAAGGCAACACGGGGG 60.078 63.158 0.00 0.00 41.41 5.40
402 403 0.108138 CTCTCTAAGGCAACACGGGG 60.108 60.000 0.00 0.00 41.41 5.73
403 404 0.108138 CCTCTCTAAGGCAACACGGG 60.108 60.000 0.00 0.00 38.67 5.28
404 405 0.108138 CCCTCTCTAAGGCAACACGG 60.108 60.000 0.00 0.00 44.71 4.94
405 406 0.895530 TCCCTCTCTAAGGCAACACG 59.104 55.000 0.00 0.00 44.71 4.49
406 407 1.404315 CGTCCCTCTCTAAGGCAACAC 60.404 57.143 0.00 0.00 44.71 3.32
407 408 0.895530 CGTCCCTCTCTAAGGCAACA 59.104 55.000 0.00 0.00 44.71 3.33
408 409 0.460459 GCGTCCCTCTCTAAGGCAAC 60.460 60.000 0.00 0.00 44.71 4.17
409 410 1.898154 GCGTCCCTCTCTAAGGCAA 59.102 57.895 0.00 0.00 44.71 4.52
410 411 2.415608 CGCGTCCCTCTCTAAGGCA 61.416 63.158 0.00 0.00 44.71 4.75
411 412 2.413765 CGCGTCCCTCTCTAAGGC 59.586 66.667 0.00 0.00 44.71 4.35
412 413 2.491022 CCCGCGTCCCTCTCTAAGG 61.491 68.421 4.92 0.00 45.77 2.69
413 414 2.491022 CCCCGCGTCCCTCTCTAAG 61.491 68.421 4.92 0.00 0.00 2.18
414 415 2.441532 CCCCGCGTCCCTCTCTAA 60.442 66.667 4.92 0.00 0.00 2.10
415 416 4.517934 CCCCCGCGTCCCTCTCTA 62.518 72.222 4.92 0.00 0.00 2.43
426 427 3.151022 CTCTCTCCTGACCCCCGC 61.151 72.222 0.00 0.00 0.00 6.13
427 428 2.305314 ATCCTCTCTCCTGACCCCCG 62.305 65.000 0.00 0.00 0.00 5.73
428 429 0.030603 AATCCTCTCTCCTGACCCCC 60.031 60.000 0.00 0.00 0.00 5.40
429 430 2.777459 TAATCCTCTCTCCTGACCCC 57.223 55.000 0.00 0.00 0.00 4.95
430 431 5.005628 ACTATAATCCTCTCTCCTGACCC 57.994 47.826 0.00 0.00 0.00 4.46
431 432 6.661805 CCTAACTATAATCCTCTCTCCTGACC 59.338 46.154 0.00 0.00 0.00 4.02
432 433 7.463431 TCCTAACTATAATCCTCTCTCCTGAC 58.537 42.308 0.00 0.00 0.00 3.51
433 434 7.649702 TCCTAACTATAATCCTCTCTCCTGA 57.350 40.000 0.00 0.00 0.00 3.86
434 435 8.713708 TTTCCTAACTATAATCCTCTCTCCTG 57.286 38.462 0.00 0.00 0.00 3.86
435 436 9.906274 ATTTTCCTAACTATAATCCTCTCTCCT 57.094 33.333 0.00 0.00 0.00 3.69
465 466 4.681483 ACGAACAAGGCTACGTAAAGTAAC 59.319 41.667 0.00 0.00 37.22 2.50
466 467 4.870363 ACGAACAAGGCTACGTAAAGTAA 58.130 39.130 0.00 0.00 37.22 2.24
467 468 4.503741 ACGAACAAGGCTACGTAAAGTA 57.496 40.909 0.00 0.00 37.22 2.24
468 469 3.375782 ACGAACAAGGCTACGTAAAGT 57.624 42.857 0.00 0.00 37.22 2.66
469 470 4.726416 TCTACGAACAAGGCTACGTAAAG 58.274 43.478 13.68 7.99 39.91 1.85
470 471 4.764679 TCTACGAACAAGGCTACGTAAA 57.235 40.909 13.68 2.97 39.91 2.01
471 472 4.439153 CCATCTACGAACAAGGCTACGTAA 60.439 45.833 13.68 8.16 39.91 3.18
472 473 3.065786 CCATCTACGAACAAGGCTACGTA 59.934 47.826 12.67 12.67 39.59 3.57
473 474 2.159282 CCATCTACGAACAAGGCTACGT 60.159 50.000 11.94 11.94 41.66 3.57
474 475 2.098607 TCCATCTACGAACAAGGCTACG 59.901 50.000 0.00 0.00 0.00 3.51
475 476 3.707793 CTCCATCTACGAACAAGGCTAC 58.292 50.000 0.00 0.00 0.00 3.58
476 477 2.100916 GCTCCATCTACGAACAAGGCTA 59.899 50.000 0.00 0.00 0.00 3.93
477 478 1.134670 GCTCCATCTACGAACAAGGCT 60.135 52.381 0.00 0.00 0.00 4.58
478 479 1.291132 GCTCCATCTACGAACAAGGC 58.709 55.000 0.00 0.00 0.00 4.35
479 480 2.672961 TGCTCCATCTACGAACAAGG 57.327 50.000 0.00 0.00 0.00 3.61
480 481 5.117745 CGATAATGCTCCATCTACGAACAAG 59.882 44.000 0.00 0.00 0.00 3.16
481 482 4.982295 CGATAATGCTCCATCTACGAACAA 59.018 41.667 0.00 0.00 0.00 2.83
482 483 4.037565 ACGATAATGCTCCATCTACGAACA 59.962 41.667 0.00 0.00 0.00 3.18
483 484 4.547532 ACGATAATGCTCCATCTACGAAC 58.452 43.478 0.00 0.00 0.00 3.95
484 485 4.848562 ACGATAATGCTCCATCTACGAA 57.151 40.909 0.00 0.00 0.00 3.85
485 486 4.848562 AACGATAATGCTCCATCTACGA 57.151 40.909 0.00 0.00 0.00 3.43
486 487 5.573282 CCTAAACGATAATGCTCCATCTACG 59.427 44.000 0.00 0.00 0.00 3.51
487 488 6.688578 TCCTAAACGATAATGCTCCATCTAC 58.311 40.000 0.00 0.00 0.00 2.59
488 489 6.911250 TCCTAAACGATAATGCTCCATCTA 57.089 37.500 0.00 0.00 0.00 1.98
489 490 5.808366 TCCTAAACGATAATGCTCCATCT 57.192 39.130 0.00 0.00 0.00 2.90
490 491 8.035394 TCTATTCCTAAACGATAATGCTCCATC 58.965 37.037 0.00 0.00 0.00 3.51
491 492 7.907389 TCTATTCCTAAACGATAATGCTCCAT 58.093 34.615 0.00 0.00 0.00 3.41
492 493 7.015292 ACTCTATTCCTAAACGATAATGCTCCA 59.985 37.037 0.00 0.00 0.00 3.86
493 494 7.379750 ACTCTATTCCTAAACGATAATGCTCC 58.620 38.462 0.00 0.00 0.00 4.70
495 496 9.862371 CATACTCTATTCCTAAACGATAATGCT 57.138 33.333 0.00 0.00 0.00 3.79
496 497 9.088512 CCATACTCTATTCCTAAACGATAATGC 57.911 37.037 0.00 0.00 0.00 3.56
499 500 9.584008 ACTCCATACTCTATTCCTAAACGATAA 57.416 33.333 0.00 0.00 0.00 1.75
501 502 9.233649 CTACTCCATACTCTATTCCTAAACGAT 57.766 37.037 0.00 0.00 0.00 3.73
502 503 8.435187 TCTACTCCATACTCTATTCCTAAACGA 58.565 37.037 0.00 0.00 0.00 3.85
503 504 8.618702 TCTACTCCATACTCTATTCCTAAACG 57.381 38.462 0.00 0.00 0.00 3.60
513 514 9.521841 CTGGTTAATCATCTACTCCATACTCTA 57.478 37.037 0.00 0.00 0.00 2.43
514 515 8.007742 ACTGGTTAATCATCTACTCCATACTCT 58.992 37.037 0.00 0.00 0.00 3.24
515 516 8.085296 CACTGGTTAATCATCTACTCCATACTC 58.915 40.741 0.00 0.00 0.00 2.59
516 517 7.785028 TCACTGGTTAATCATCTACTCCATACT 59.215 37.037 0.00 0.00 0.00 2.12
517 518 7.952671 TCACTGGTTAATCATCTACTCCATAC 58.047 38.462 0.00 0.00 0.00 2.39
518 519 8.727100 ATCACTGGTTAATCATCTACTCCATA 57.273 34.615 0.00 0.00 0.00 2.74
519 520 7.623999 ATCACTGGTTAATCATCTACTCCAT 57.376 36.000 0.00 0.00 0.00 3.41
520 521 8.547481 TTATCACTGGTTAATCATCTACTCCA 57.453 34.615 0.00 0.00 0.00 3.86
528 529 9.801873 CCGAAAAATTTATCACTGGTTAATCAT 57.198 29.630 0.00 0.00 0.00 2.45
529 530 9.015367 TCCGAAAAATTTATCACTGGTTAATCA 57.985 29.630 0.00 0.00 0.00 2.57
530 531 9.503427 CTCCGAAAAATTTATCACTGGTTAATC 57.497 33.333 0.00 0.00 0.00 1.75
531 532 9.020731 ACTCCGAAAAATTTATCACTGGTTAAT 57.979 29.630 0.00 0.00 0.00 1.40
532 533 8.398878 ACTCCGAAAAATTTATCACTGGTTAA 57.601 30.769 0.00 0.00 0.00 2.01
533 534 7.881232 AGACTCCGAAAAATTTATCACTGGTTA 59.119 33.333 0.00 0.00 0.00 2.85
534 535 6.715264 AGACTCCGAAAAATTTATCACTGGTT 59.285 34.615 0.00 0.00 0.00 3.67
535 536 6.149474 CAGACTCCGAAAAATTTATCACTGGT 59.851 38.462 0.00 0.00 0.00 4.00
536 537 6.149474 ACAGACTCCGAAAAATTTATCACTGG 59.851 38.462 0.00 0.00 0.00 4.00
537 538 7.133891 ACAGACTCCGAAAAATTTATCACTG 57.866 36.000 0.00 0.00 0.00 3.66
538 539 6.090898 CGACAGACTCCGAAAAATTTATCACT 59.909 38.462 0.00 0.00 0.00 3.41
539 540 6.090358 TCGACAGACTCCGAAAAATTTATCAC 59.910 38.462 0.00 0.00 0.00 3.06
540 541 6.090358 GTCGACAGACTCCGAAAAATTTATCA 59.910 38.462 11.55 0.00 43.80 2.15
541 542 6.467648 GTCGACAGACTCCGAAAAATTTATC 58.532 40.000 11.55 0.00 43.80 1.75
542 543 6.404712 GTCGACAGACTCCGAAAAATTTAT 57.595 37.500 11.55 0.00 43.80 1.40
543 544 5.834239 GTCGACAGACTCCGAAAAATTTA 57.166 39.130 11.55 0.00 43.80 1.40
567 568 7.066781 TCAGAGGAAAGGGTTCAAAAATTAGT 58.933 34.615 0.00 0.00 35.25 2.24
568 569 7.524717 TCAGAGGAAAGGGTTCAAAAATTAG 57.475 36.000 0.00 0.00 35.25 1.73
569 570 7.728083 TGATCAGAGGAAAGGGTTCAAAAATTA 59.272 33.333 0.00 0.00 35.25 1.40
576 577 4.722526 TTTGATCAGAGGAAAGGGTTCA 57.277 40.909 0.00 0.00 35.25 3.18
577 578 6.596309 AATTTTGATCAGAGGAAAGGGTTC 57.404 37.500 0.00 0.00 0.00 3.62
666 670 1.599606 GAGTGAGAAGAGGCTCGCCA 61.600 60.000 9.22 3.12 44.43 5.69
726 730 1.771565 ATGACATGTGGGGCTCATTG 58.228 50.000 1.15 0.00 0.00 2.82
733 737 2.620115 GTGCTATCAATGACATGTGGGG 59.380 50.000 1.15 0.00 0.00 4.96
773 778 3.440415 GGTTTGCCTAGCCACCGC 61.440 66.667 0.00 0.00 0.00 5.68
792 797 2.485814 GGTGACATGGACTCTTTGCTTC 59.514 50.000 0.00 0.00 0.00 3.86
843 848 4.231439 GTTGCTGGGGTTTTAATACGTTG 58.769 43.478 0.00 0.00 0.00 4.10
1002 1007 0.106619 ACTGGGGAGTAGCCGAGTAG 60.107 60.000 0.00 0.00 37.63 2.57
1557 1569 3.256960 GACTTGGGGGTGGAGCCA 61.257 66.667 0.00 0.00 39.65 4.75
1848 1866 2.125912 GCGATGAGCTGGACGTGT 60.126 61.111 0.00 0.00 44.04 4.49
1880 1898 1.347707 AGAATGAGGCGTTCAGGAACA 59.652 47.619 12.22 0.00 41.20 3.18
1887 1905 3.400007 GGCGAGAATGAGGCGTTC 58.600 61.111 0.00 0.00 0.00 3.95
1898 1916 4.373116 GCCTGAACACCGGCGAGA 62.373 66.667 9.30 0.00 36.45 4.04
2076 2100 1.227527 CATCTCCACGGCGCCATTA 60.228 57.895 28.98 7.46 0.00 1.90
2151 2175 1.343465 CTGGGACTAAACCTGTCACGT 59.657 52.381 0.00 0.00 40.46 4.49
2293 2331 9.578576 AGGTATCATAATAGTGAATGTTGCAAT 57.421 29.630 0.59 0.00 0.00 3.56
2449 2487 1.068127 GCCAAATCCCATGATGAGCAC 59.932 52.381 0.00 0.00 0.00 4.40
2552 2604 4.082125 AGCTTAATGGAGTTGTTTCCCAG 58.918 43.478 0.00 0.00 36.35 4.45
2575 2627 9.844257 TTTATGTATCATATGTGGTCAATGTCA 57.156 29.630 1.90 0.00 0.00 3.58
2688 2740 6.148150 TGGTAAAGTACTAACTTGCGGAAATG 59.852 38.462 0.00 0.00 45.37 2.32
2717 2769 3.503827 TCAGTGAGTATTGTAGCCACG 57.496 47.619 0.00 0.00 33.37 4.94
2758 2810 6.043590 AGCACATCCATAGAATGTTATCTGGA 59.956 38.462 0.00 0.00 0.00 3.86
2759 2811 6.236409 AGCACATCCATAGAATGTTATCTGG 58.764 40.000 0.00 0.00 0.00 3.86
2883 2935 2.699846 TCATCCAGCCCATTAATTTGGC 59.300 45.455 15.15 15.15 45.70 4.52
3032 3084 3.885724 TGACGAGGCATCATTTAGACA 57.114 42.857 0.00 0.00 0.00 3.41
3072 3124 4.141274 AGGCCATACCACATACAGCATTTA 60.141 41.667 5.01 0.00 43.14 1.40
3073 3125 2.958355 GGCCATACCACATACAGCATTT 59.042 45.455 0.00 0.00 38.86 2.32
3074 3126 2.175499 AGGCCATACCACATACAGCATT 59.825 45.455 5.01 0.00 43.14 3.56
3076 3128 1.212375 AGGCCATACCACATACAGCA 58.788 50.000 5.01 0.00 43.14 4.41
3077 3129 1.949525 CAAGGCCATACCACATACAGC 59.050 52.381 5.01 0.00 43.14 4.40
3078 3130 3.118261 AGTCAAGGCCATACCACATACAG 60.118 47.826 5.01 0.00 43.14 2.74
3119 3179 2.102925 ACTTTTCTGGGCAACATGTTGG 59.897 45.455 33.56 20.08 40.74 3.77
3201 3261 5.535783 TGGTTGTAGATTTGGCCATCATATG 59.464 40.000 6.09 0.00 0.00 1.78
3338 3398 3.244976 CAAAAATTAGCAAGTGAGGGCG 58.755 45.455 0.00 0.00 34.54 6.13
3579 3640 0.253044 ACTGCAGCACCACGGATAAT 59.747 50.000 15.27 0.00 0.00 1.28
3608 3669 4.312443 GCCATGGCTTCATATTTCCATTG 58.688 43.478 29.98 0.00 37.22 2.82
4054 4137 7.166804 CAGTAACCGTTGGTGAAACAAAATAAG 59.833 37.037 0.00 0.00 39.98 1.73
4055 4138 6.973474 CAGTAACCGTTGGTGAAACAAAATAA 59.027 34.615 0.00 0.00 39.98 1.40
4056 4139 6.318144 TCAGTAACCGTTGGTGAAACAAAATA 59.682 34.615 0.00 0.00 39.98 1.40
4103 4186 3.129813 CACAACATGGCAGCATCATACTT 59.870 43.478 0.00 0.00 0.00 2.24
4136 4219 3.198417 TGCTGATGAAGAGCCAATCTACA 59.802 43.478 0.00 0.00 37.23 2.74
4147 4230 7.667219 ACCTTTAGAAGAAATTGCTGATGAAGA 59.333 33.333 4.89 0.00 0.00 2.87
4162 4245 7.170998 GTCTTCGAATGAACAACCTTTAGAAGA 59.829 37.037 0.00 0.00 38.40 2.87
4171 4254 2.808543 AGCAGTCTTCGAATGAACAACC 59.191 45.455 0.00 0.00 28.30 3.77
4276 4359 7.663905 ACACTAAATGCCTACAGTCACATAAAA 59.336 33.333 0.00 0.00 0.00 1.52
4334 4417 1.747709 TAGTCGTTCGAGGGGAAGAG 58.252 55.000 0.00 0.00 34.69 2.85
4347 4430 9.578439 GTGATAAGTACCAAAGTATTTAGTCGT 57.422 33.333 0.00 0.00 35.03 4.34
4348 4431 9.798994 AGTGATAAGTACCAAAGTATTTAGTCG 57.201 33.333 0.00 0.00 35.03 4.18
4408 4500 9.784680 CAAGCAATGGAGATAATAAATAGATGC 57.215 33.333 0.00 0.00 0.00 3.91
4438 4530 2.472488 CGGTGCAAGTTTGATGAAAAGC 59.528 45.455 0.00 0.00 0.00 3.51
4578 4670 7.164122 TCAAATCCAACCTGCTCATAGATATC 58.836 38.462 0.00 0.00 0.00 1.63
4579 4671 7.083062 TCAAATCCAACCTGCTCATAGATAT 57.917 36.000 0.00 0.00 0.00 1.63
4585 4677 5.954150 AGTAAATCAAATCCAACCTGCTCAT 59.046 36.000 0.00 0.00 0.00 2.90
4598 4690 8.524487 AGTTCTCAGACTCGTAGTAAATCAAAT 58.476 33.333 0.00 0.00 0.00 2.32
4739 4832 2.092291 ATGGTGCGCAACGTAGACG 61.092 57.895 20.83 0.00 46.33 4.18
4802 4897 6.365789 CGAATTGTGCCACATTCTAAACATTT 59.634 34.615 0.00 0.00 0.00 2.32
4846 4941 3.320826 CCCCATTTAACGGATTTCCATCC 59.679 47.826 0.00 0.00 45.40 3.51
4875 4970 8.934507 TCCCTTGTTTTTACATGTTTTAACAG 57.065 30.769 2.30 6.44 43.04 3.16
5026 5122 4.590850 ATGAAACTGCCTCAAAAGGAAC 57.409 40.909 0.00 0.00 46.67 3.62


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

AutoCloner maintained by Alex Coulton.