Multiple sequence alignment - TraesCS6B01G171600

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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 TraesCS6B01G171600 chr6B 100.000 4772 0 0 1 4772 184144022 184148793 0.000000e+00 8813.0
1 TraesCS6B01G171600 chr6D 96.539 2427 59 8 1668 4073 99790491 99792913 0.000000e+00 3993.0
2 TraesCS6B01G171600 chr6D 92.071 845 31 16 854 1672 99789612 99790446 0.000000e+00 1157.0
3 TraesCS6B01G171600 chr6D 84.683 568 62 9 76 627 99788622 99789180 1.170000e-150 544.0
4 TraesCS6B01G171600 chr6D 91.774 389 16 4 4393 4771 99793412 99793794 1.180000e-145 527.0
5 TraesCS6B01G171600 chr6D 92.237 219 16 1 4178 4395 99793114 99793332 4.640000e-80 309.0
6 TraesCS6B01G171600 chr6D 82.558 344 29 10 3586 3906 100348735 100349070 1.690000e-69 274.0
7 TraesCS6B01G171600 chr6D 86.992 246 21 4 4536 4770 100349853 100350098 2.830000e-67 267.0
8 TraesCS6B01G171600 chr6D 90.500 200 16 2 625 823 99789415 99789612 1.320000e-65 261.0
9 TraesCS6B01G171600 chr6D 90.526 95 6 3 2 94 157286591 157286684 6.490000e-24 122.0
10 TraesCS6B01G171600 chr6A 93.883 1782 64 23 656 2413 119749761 119751521 0.000000e+00 2645.0
11 TraesCS6B01G171600 chr6A 92.641 992 49 5 3100 4073 119752486 119753471 0.000000e+00 1406.0
12 TraesCS6B01G171600 chr6A 97.118 694 17 3 2412 3103 119751616 119752308 0.000000e+00 1168.0
13 TraesCS6B01G171600 chr6A 85.397 630 52 17 4178 4772 119753720 119754344 6.790000e-173 617.0
14 TraesCS6B01G171600 chr2D 78.694 291 48 9 89 366 608982392 608982681 1.050000e-41 182.0
15 TraesCS6B01G171600 chr2D 84.431 167 24 2 196 361 575177075 575176910 3.820000e-36 163.0
16 TraesCS6B01G171600 chr2D 77.551 294 45 9 88 361 429043265 429043557 1.780000e-34 158.0
17 TraesCS6B01G171600 chr2D 89.109 101 7 4 1 101 80942411 80942315 6.490000e-24 122.0
18 TraesCS6B01G171600 chr1B 76.161 323 56 9 88 389 334247441 334247119 2.970000e-32 150.0
19 TraesCS6B01G171600 chr1B 81.111 180 34 0 175 354 678866954 678867133 1.380000e-30 145.0
20 TraesCS6B01G171600 chr1B 91.463 82 7 0 91 172 95369321 95369402 3.900000e-21 113.0
21 TraesCS6B01G171600 chr1B 85.000 80 12 0 81 160 556266178 556266257 1.100000e-11 82.4
22 TraesCS6B01G171600 chr1B 83.750 80 13 0 81 160 556299747 556299826 5.120000e-10 76.8
23 TraesCS6B01G171600 chr7D 78.440 218 45 2 173 389 562433464 562433248 1.790000e-29 141.0
24 TraesCS6B01G171600 chr7D 92.222 90 3 3 1 89 84776133 84776219 1.800000e-24 124.0
25 TraesCS6B01G171600 chr5B 77.828 221 46 3 170 389 530964206 530963988 3.000000e-27 134.0
26 TraesCS6B01G171600 chr4D 79.474 190 36 3 201 389 473829771 473829958 1.080000e-26 132.0
27 TraesCS6B01G171600 chr4D 87.356 87 6 4 87 172 5682736 5682654 1.410000e-15 95.3
28 TraesCS6B01G171600 chr1A 96.296 81 2 1 1 81 337531770 337531849 1.080000e-26 132.0
29 TraesCS6B01G171600 chr1A 74.923 323 55 9 88 387 369999018 369999337 1.800000e-24 124.0
30 TraesCS6B01G171600 chr1D 92.222 90 5 2 1 89 61623241 61623153 5.010000e-25 126.0
31 TraesCS6B01G171600 chr1D 72.564 390 76 17 75 443 25718141 25717762 1.090000e-16 99.0
32 TraesCS6B01G171600 chr3D 91.398 93 5 2 1 90 427776715 427776807 1.800000e-24 124.0
33 TraesCS6B01G171600 chr7B 90.426 94 6 2 1 94 343461396 343461306 2.330000e-23 121.0
34 TraesCS6B01G171600 chr2B 89.583 96 8 2 1 95 164505501 164505407 2.330000e-23 121.0
35 TraesCS6B01G171600 chr5A 88.889 99 7 3 1 98 157361098 157361193 8.390000e-23 119.0
36 TraesCS6B01G171600 chr5A 77.215 158 32 3 195 351 456080261 456080415 6.580000e-14 89.8


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 TraesCS6B01G171600 chr6B 184144022 184148793 4771 False 8813.000000 8813 100.000000 1 4772 1 chr6B.!!$F1 4771
1 TraesCS6B01G171600 chr6D 99788622 99793794 5172 False 1131.833333 3993 91.300667 76 4771 6 chr6D.!!$F2 4695
2 TraesCS6B01G171600 chr6D 100348735 100350098 1363 False 270.500000 274 84.775000 3586 4770 2 chr6D.!!$F3 1184
3 TraesCS6B01G171600 chr6A 119749761 119754344 4583 False 1459.000000 2645 92.259750 656 4772 4 chr6A.!!$F1 4116

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
34 35 0.037232 AGCCTTAGACGCACAGTTCC 60.037 55.0 0.00 0.0 0.0 3.62 F
38 39 0.038892 TTAGACGCACAGTTCCGGAC 60.039 55.0 1.83 0.0 0.0 4.79 F
1029 1300 0.182299 TGAGATGCACCAACCACACA 59.818 50.0 0.00 0.0 0.0 3.72 F
2050 2389 0.035152 AGGGAAGCATTGACATCGCA 60.035 50.0 0.00 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2369 0.659957 GCGATGTCAATGCTTCCCTC 59.340 55.000 0.0 0.0 0.00 4.30 R
2050 2389 3.118956 GGACATCTTTCATCGAGTGGACT 60.119 47.826 0.0 0.0 0.00 3.85 R
2731 3171 1.401761 TGTTGCAGTTTCTGGCATGT 58.598 45.000 0.0 0.0 40.17 3.21 R
3896 4549 1.135199 TGTTCTAAGCTCTAACCCGCG 60.135 52.381 0.0 0.0 0.00 6.46 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
20 21 3.356529 CCTTCTGTTACCATCAGCCTT 57.643 47.619 0.00 0.00 33.48 4.35
21 22 4.487714 CCTTCTGTTACCATCAGCCTTA 57.512 45.455 0.00 0.00 33.48 2.69
22 23 4.446371 CCTTCTGTTACCATCAGCCTTAG 58.554 47.826 0.00 0.00 33.48 2.18
23 24 4.162320 CCTTCTGTTACCATCAGCCTTAGA 59.838 45.833 0.00 0.00 33.48 2.10
24 25 4.737855 TCTGTTACCATCAGCCTTAGAC 57.262 45.455 0.00 0.00 33.48 2.59
25 26 3.130516 TCTGTTACCATCAGCCTTAGACG 59.869 47.826 0.00 0.00 33.48 4.18
26 27 2.202566 GTTACCATCAGCCTTAGACGC 58.797 52.381 0.00 0.00 0.00 5.19
27 28 1.480789 TACCATCAGCCTTAGACGCA 58.519 50.000 0.00 0.00 0.00 5.24
28 29 0.108138 ACCATCAGCCTTAGACGCAC 60.108 55.000 0.00 0.00 0.00 5.34
29 30 0.108186 CCATCAGCCTTAGACGCACA 60.108 55.000 0.00 0.00 0.00 4.57
30 31 1.284657 CATCAGCCTTAGACGCACAG 58.715 55.000 0.00 0.00 0.00 3.66
31 32 0.898320 ATCAGCCTTAGACGCACAGT 59.102 50.000 0.00 0.00 0.00 3.55
32 33 0.679505 TCAGCCTTAGACGCACAGTT 59.320 50.000 0.00 0.00 0.00 3.16
33 34 1.071605 CAGCCTTAGACGCACAGTTC 58.928 55.000 0.00 0.00 0.00 3.01
34 35 0.037232 AGCCTTAGACGCACAGTTCC 60.037 55.000 0.00 0.00 0.00 3.62
35 36 1.352156 GCCTTAGACGCACAGTTCCG 61.352 60.000 0.00 0.00 0.00 4.30
36 37 0.736325 CCTTAGACGCACAGTTCCGG 60.736 60.000 0.00 0.00 0.00 5.14
37 38 0.242825 CTTAGACGCACAGTTCCGGA 59.757 55.000 0.00 0.00 0.00 5.14
38 39 0.038892 TTAGACGCACAGTTCCGGAC 60.039 55.000 1.83 0.00 0.00 4.79
39 40 1.870055 TAGACGCACAGTTCCGGACC 61.870 60.000 1.83 0.00 0.00 4.46
40 41 4.309950 ACGCACAGTTCCGGACCC 62.310 66.667 1.83 0.00 0.00 4.46
42 43 4.717313 GCACAGTTCCGGACCCCC 62.717 72.222 1.83 0.00 0.00 5.40
43 44 2.928396 CACAGTTCCGGACCCCCT 60.928 66.667 1.83 0.00 0.00 4.79
44 45 1.611261 CACAGTTCCGGACCCCCTA 60.611 63.158 1.83 0.00 0.00 3.53
45 46 1.611556 ACAGTTCCGGACCCCCTAC 60.612 63.158 1.83 0.00 0.00 3.18
46 47 2.040114 AGTTCCGGACCCCCTACC 59.960 66.667 1.83 0.00 0.00 3.18
47 48 3.085947 GTTCCGGACCCCCTACCC 61.086 72.222 1.83 0.00 0.00 3.69
48 49 4.783501 TTCCGGACCCCCTACCCG 62.784 72.222 1.83 0.00 42.64 5.28
51 52 4.133373 CGGACCCCCTACCCGAGA 62.133 72.222 0.00 0.00 45.58 4.04
52 53 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
53 54 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
54 55 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
55 56 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
56 57 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
57 58 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
58 59 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
59 60 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
60 61 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
62 63 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
63 64 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
64 65 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
65 66 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
66 67 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
67 68 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
68 69 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
69 70 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
86 87 1.416401 CACCGACATAATGGCCCTACT 59.584 52.381 0.00 0.00 0.00 2.57
105 106 2.280797 GACCAGCGCACCAGAACA 60.281 61.111 11.47 0.00 0.00 3.18
106 107 1.891919 GACCAGCGCACCAGAACAA 60.892 57.895 11.47 0.00 0.00 2.83
107 108 2.117941 GACCAGCGCACCAGAACAAC 62.118 60.000 11.47 0.00 0.00 3.32
108 109 2.186160 CCAGCGCACCAGAACAACA 61.186 57.895 11.47 0.00 0.00 3.33
109 110 1.723608 CCAGCGCACCAGAACAACAA 61.724 55.000 11.47 0.00 0.00 2.83
110 111 0.592247 CAGCGCACCAGAACAACAAC 60.592 55.000 11.47 0.00 0.00 3.32
111 112 0.748005 AGCGCACCAGAACAACAACT 60.748 50.000 11.47 0.00 0.00 3.16
112 113 0.941542 GCGCACCAGAACAACAACTA 59.058 50.000 0.30 0.00 0.00 2.24
113 114 1.333791 GCGCACCAGAACAACAACTAC 60.334 52.381 0.30 0.00 0.00 2.73
114 115 2.210116 CGCACCAGAACAACAACTACT 58.790 47.619 0.00 0.00 0.00 2.57
115 116 3.386486 CGCACCAGAACAACAACTACTA 58.614 45.455 0.00 0.00 0.00 1.82
124 125 6.089551 CAGAACAACAACTACTACCGATGAAG 59.910 42.308 0.00 0.00 0.00 3.02
131 132 2.853731 ACTACCGATGAAGAGAAGCG 57.146 50.000 0.00 0.00 0.00 4.68
135 136 2.093106 ACCGATGAAGAGAAGCGTAGT 58.907 47.619 0.00 0.00 0.00 2.73
138 139 3.427638 CCGATGAAGAGAAGCGTAGTTCA 60.428 47.826 0.00 0.00 0.00 3.18
163 164 2.549992 GCATCCAACCTGTAGACACACA 60.550 50.000 0.00 0.00 0.00 3.72
166 167 3.537580 TCCAACCTGTAGACACACAAAC 58.462 45.455 0.00 0.00 0.00 2.93
168 169 3.882888 CCAACCTGTAGACACACAAACAT 59.117 43.478 0.00 0.00 0.00 2.71
169 170 5.060506 CCAACCTGTAGACACACAAACATA 58.939 41.667 0.00 0.00 0.00 2.29
172 173 6.360370 ACCTGTAGACACACAAACATAGAT 57.640 37.500 0.00 0.00 0.00 1.98
179 180 5.127845 AGACACACAAACATAGATCGGATCT 59.872 40.000 22.96 22.96 43.33 2.75
182 183 5.692204 CACACAAACATAGATCGGATCTACC 59.308 44.000 25.68 0.00 44.07 3.18
207 208 3.055675 AGTTAAATGTCGACCGAATCCCA 60.056 43.478 14.12 0.00 0.00 4.37
247 248 3.164977 TCCACACGCCCTCCAACA 61.165 61.111 0.00 0.00 0.00 3.33
251 252 4.025401 CACGCCCTCCAACAACGC 62.025 66.667 0.00 0.00 0.00 4.84
263 264 0.249741 AACAACGCTAGAAGCACCGT 60.250 50.000 0.00 0.00 42.58 4.83
269 270 1.726853 GCTAGAAGCACCGTTGTGAT 58.273 50.000 0.00 0.00 45.76 3.06
271 272 2.002586 CTAGAAGCACCGTTGTGATGG 58.997 52.381 0.00 0.00 45.76 3.51
273 274 2.200170 GAAGCACCGTTGTGATGGGC 62.200 60.000 0.00 0.00 45.76 5.36
274 275 4.101790 GCACCGTTGTGATGGGCG 62.102 66.667 0.00 0.00 45.76 6.13
303 304 4.494199 CGGCGATAACCTTGTTTCATCTTC 60.494 45.833 0.00 0.00 0.00 2.87
311 312 4.279420 ACCTTGTTTCATCTTCAAAGAGCC 59.721 41.667 0.00 0.00 38.66 4.70
318 319 0.324614 TCTTCAAAGAGCCGCCATCA 59.675 50.000 0.00 0.00 0.00 3.07
319 320 0.449388 CTTCAAAGAGCCGCCATCAC 59.551 55.000 0.00 0.00 0.00 3.06
324 325 2.045926 GAGCCGCCATCACCTTGT 60.046 61.111 0.00 0.00 0.00 3.16
330 331 0.534412 CGCCATCACCTTGTCTCTCT 59.466 55.000 0.00 0.00 0.00 3.10
333 334 2.027745 GCCATCACCTTGTCTCTCTGAA 60.028 50.000 0.00 0.00 0.00 3.02
336 337 4.244066 CATCACCTTGTCTCTCTGAACAG 58.756 47.826 0.00 0.00 0.00 3.16
339 340 2.630580 ACCTTGTCTCTCTGAACAGGAC 59.369 50.000 1.93 3.05 32.86 3.85
345 346 4.081142 TGTCTCTCTGAACAGGACACAAAA 60.081 41.667 7.80 0.00 32.91 2.44
356 357 5.716094 ACAGGACACAAAACCTAACAAAAC 58.284 37.500 0.00 0.00 34.87 2.43
360 361 6.209788 AGGACACAAAACCTAACAAAACTCAA 59.790 34.615 0.00 0.00 34.47 3.02
361 362 6.530181 GGACACAAAACCTAACAAAACTCAAG 59.470 38.462 0.00 0.00 0.00 3.02
365 366 8.432359 CACAAAACCTAACAAAACTCAAGAAAC 58.568 33.333 0.00 0.00 0.00 2.78
381 382 7.657354 ACTCAAGAAACCATCCAAAAATAAAGC 59.343 33.333 0.00 0.00 0.00 3.51
387 388 3.134623 CCATCCAAAAATAAAGCCCTCCC 59.865 47.826 0.00 0.00 0.00 4.30
399 415 3.075005 CCTCCCGATCCACCGTGT 61.075 66.667 0.00 0.00 0.00 4.49
414 430 1.414181 CCGTGTCTCCATGGCTCTAAT 59.586 52.381 6.96 0.00 40.78 1.73
433 449 7.309744 GCTCTAATACTACAAGAGATGAGGCAT 60.310 40.741 2.86 0.00 39.29 4.40
438 454 1.414181 ACAAGAGATGAGGCATACCGG 59.586 52.381 0.00 0.00 42.76 5.28
458 474 4.025401 GCACAGGAAACCCACGCG 62.025 66.667 3.53 3.53 0.00 6.01
459 475 3.353836 CACAGGAAACCCACGCGG 61.354 66.667 12.47 0.00 37.81 6.46
478 494 1.228003 CGGGGTGCCTTTGTGTACA 60.228 57.895 0.00 0.00 0.00 2.90
487 503 1.535462 CCTTTGTGTACAAGCGAAGGG 59.465 52.381 18.72 7.80 40.76 3.95
494 510 1.134877 GTACAAGCGAAGGGGTACTCC 60.135 57.143 2.47 2.47 34.68 3.85
509 525 7.068061 AGGGGTACTCCTTAATACTTAGTCAG 58.932 42.308 9.09 0.00 32.13 3.51
512 528 7.201835 GGTACTCCTTAATACTTAGTCAGTGC 58.798 42.308 0.00 0.00 35.97 4.40
517 533 9.167311 CTCCTTAATACTTAGTCAGTGCAAAAT 57.833 33.333 0.00 0.00 35.97 1.82
569 585 8.682936 AAGATAAATCTTCCGTCATGCTAAAT 57.317 30.769 0.00 0.00 43.27 1.40
577 593 6.599244 TCTTCCGTCATGCTAAATTCATCTTT 59.401 34.615 0.00 0.00 0.00 2.52
662 915 7.776618 ATAACGTGGATTGATATCTACTCCA 57.223 36.000 13.94 13.94 39.40 3.86
680 933 5.611374 ACTCCATTCGTCCCATAATGTAAG 58.389 41.667 0.00 0.00 32.34 2.34
761 1014 3.334583 AAGAGCTGAATAAACCGCAGA 57.665 42.857 0.00 0.00 0.00 4.26
764 1017 3.437049 AGAGCTGAATAAACCGCAGAAAC 59.563 43.478 0.00 0.00 0.00 2.78
766 1019 2.488153 GCTGAATAAACCGCAGAAACCT 59.512 45.455 0.00 0.00 0.00 3.50
767 1020 3.687698 GCTGAATAAACCGCAGAAACCTA 59.312 43.478 0.00 0.00 0.00 3.08
787 1040 9.628500 AAACCTATACAAGATCCAATAAACCTC 57.372 33.333 0.00 0.00 0.00 3.85
817 1074 4.367166 TCTCTCTCCCTCTGTTCTCTCTA 58.633 47.826 0.00 0.00 0.00 2.43
837 1094 6.961360 TCTACACTAGAGAGAGAGAGAGAG 57.039 45.833 0.00 0.00 0.00 3.20
838 1095 6.669631 TCTACACTAGAGAGAGAGAGAGAGA 58.330 44.000 0.00 0.00 0.00 3.10
839 1096 5.860941 ACACTAGAGAGAGAGAGAGAGAG 57.139 47.826 0.00 0.00 0.00 3.20
840 1097 4.651503 ACACTAGAGAGAGAGAGAGAGAGG 59.348 50.000 0.00 0.00 0.00 3.69
841 1098 4.895889 CACTAGAGAGAGAGAGAGAGAGGA 59.104 50.000 0.00 0.00 0.00 3.71
842 1099 5.010516 CACTAGAGAGAGAGAGAGAGAGGAG 59.989 52.000 0.00 0.00 0.00 3.69
843 1100 4.000928 AGAGAGAGAGAGAGAGAGGAGT 57.999 50.000 0.00 0.00 0.00 3.85
906 1164 3.765257 ATCCCTCCGCCCTCTCCAG 62.765 68.421 0.00 0.00 0.00 3.86
908 1166 3.151022 CCTCCGCCCTCTCCAGAC 61.151 72.222 0.00 0.00 0.00 3.51
1029 1300 0.182299 TGAGATGCACCAACCACACA 59.818 50.000 0.00 0.00 0.00 3.72
1223 1508 2.875933 GTGTCAACTCGGTTGGATTTGA 59.124 45.455 14.23 0.00 42.99 2.69
1329 1616 1.359848 CGATTGCGTTTCTAGGTGCT 58.640 50.000 0.00 0.00 0.00 4.40
1346 1633 4.349048 AGGTGCTAGATATTGCCTGATTCA 59.651 41.667 0.00 0.00 0.00 2.57
1394 1682 1.959282 GGATCTGCATTTTAGCTGGGG 59.041 52.381 0.00 0.00 34.63 4.96
1407 1695 0.462789 GCTGGGGCTTTGATGGAATG 59.537 55.000 0.00 0.00 35.22 2.67
1417 1705 4.751060 CTTTGATGGAATGGTGGAACATG 58.249 43.478 0.00 0.00 44.52 3.21
1427 1715 1.024579 GTGGAACATGGGTAGCACCG 61.025 60.000 0.00 0.00 44.52 4.94
1459 1747 8.365399 TGACCTTAATCGTGCTAAATAATGAG 57.635 34.615 0.00 0.00 0.00 2.90
1517 1805 0.391130 CAGCTCGATTCGGGGTCAAA 60.391 55.000 7.84 0.00 35.25 2.69
1573 1862 1.966451 GCTCTGGGTTTCACGTGGG 60.966 63.158 17.00 0.00 0.00 4.61
1606 1895 0.184933 TGGTGTAGCTTTTGGCCACT 59.815 50.000 3.88 0.69 43.05 4.00
1632 1921 7.417612 TCTTGCTTGTTTTGTCTTAGTGAATC 58.582 34.615 0.00 0.00 0.00 2.52
1633 1922 6.072112 TGCTTGTTTTGTCTTAGTGAATCC 57.928 37.500 0.00 0.00 0.00 3.01
1634 1923 5.009610 TGCTTGTTTTGTCTTAGTGAATCCC 59.990 40.000 0.00 0.00 0.00 3.85
1635 1924 5.009610 GCTTGTTTTGTCTTAGTGAATCCCA 59.990 40.000 0.00 0.00 0.00 4.37
1636 1925 6.294731 GCTTGTTTTGTCTTAGTGAATCCCAT 60.295 38.462 0.00 0.00 0.00 4.00
1680 2018 0.603707 TGAGTTGCTTCGGCCTTCAG 60.604 55.000 0.00 0.00 40.91 3.02
2030 2369 1.000827 AGATAGACGATGCGCTCTTGG 60.001 52.381 9.73 0.00 0.00 3.61
2050 2389 0.035152 AGGGAAGCATTGACATCGCA 60.035 50.000 0.00 0.00 0.00 5.10
2438 2873 4.706476 TCACAGATTGCTATTTTGAAGGGG 59.294 41.667 1.79 0.00 0.00 4.79
2441 2876 3.448660 AGATTGCTATTTTGAAGGGGTGC 59.551 43.478 0.00 0.00 0.00 5.01
2452 2887 1.541588 GAAGGGGTGCTGTTTCATGTC 59.458 52.381 0.00 0.00 0.00 3.06
2479 2914 1.135286 GTGCCAAGCAGTATTCTTGCC 60.135 52.381 0.00 0.00 38.05 4.52
2480 2915 1.176527 GCCAAGCAGTATTCTTGCCA 58.823 50.000 0.00 0.00 38.05 4.92
2481 2916 1.545582 GCCAAGCAGTATTCTTGCCAA 59.454 47.619 0.00 0.00 38.05 4.52
2731 3171 2.633967 TGGCTGGACTAAAACGGTTAGA 59.366 45.455 13.32 0.00 0.00 2.10
3020 3460 4.799564 TTTGTGGTCTTTATTGGCCATC 57.200 40.909 6.09 0.00 33.20 3.51
3327 3954 6.479095 TTGCCTGAGTTTTTCTTTTGTTTG 57.521 33.333 0.00 0.00 0.00 2.93
3337 3964 7.277760 AGTTTTTCTTTTGTTTGCACCATCTAC 59.722 33.333 0.00 0.00 0.00 2.59
3447 4075 5.125100 TGTTGCATGTGAAAGAGAATTCC 57.875 39.130 0.65 0.00 0.00 3.01
3563 4191 5.655394 TCACCAGATGGCTCTATAGGTATT 58.345 41.667 0.00 0.00 39.32 1.89
3702 4354 3.057969 TCTTTTGATGACATGGTCGCT 57.942 42.857 0.00 0.00 34.95 4.93
3708 4360 2.562738 TGATGACATGGTCGCTATAGGG 59.437 50.000 10.48 10.48 34.95 3.53
3738 4390 2.287308 CGGCCACGAACTGAAATCAAAA 60.287 45.455 2.24 0.00 44.60 2.44
3866 4519 3.873910 ACCACATATTGAGCTGTACCAC 58.126 45.455 0.00 0.00 0.00 4.16
3869 4522 3.798878 CACATATTGAGCTGTACCACTCG 59.201 47.826 0.00 0.00 35.61 4.18
3907 4560 2.894240 TTTAGCGCCGCGGGTTAGAG 62.894 60.000 29.38 2.50 0.00 2.43
3922 4575 3.925299 GGTTAGAGCTTAGAACACGGTTC 59.075 47.826 8.26 8.26 0.00 3.62
3963 4631 1.357991 GAAGAGGCTTCTGCTCGCAC 61.358 60.000 0.00 0.00 39.59 5.34
3965 4633 1.809209 GAGGCTTCTGCTCGCACTC 60.809 63.158 0.00 0.00 39.59 3.51
3966 4634 2.047844 GGCTTCTGCTCGCACTCA 60.048 61.111 0.00 0.00 39.59 3.41
4036 4704 5.934935 TCAAGAAATAACCGGTTCTGAAC 57.065 39.130 26.16 12.05 34.33 3.18
4039 4707 5.223449 AGAAATAACCGGTTCTGAACTCA 57.777 39.130 26.16 3.39 32.84 3.41
4051 4719 3.554934 TCTGAACTCACTGTTTGCCAAT 58.445 40.909 0.00 0.00 39.30 3.16
4133 5075 8.844865 TGCCAGGATAGTACAATCATATCTAT 57.155 34.615 0.00 0.00 0.00 1.98
4172 5193 7.275560 ACAAAAAGTCATGTTAAAGTCTTGCAC 59.724 33.333 0.00 0.00 0.00 4.57
4173 5194 6.449635 AAAGTCATGTTAAAGTCTTGCACA 57.550 33.333 0.00 0.69 0.00 4.57
4174 5195 5.679734 AGTCATGTTAAAGTCTTGCACAG 57.320 39.130 0.00 0.00 0.00 3.66
4175 5196 4.516698 AGTCATGTTAAAGTCTTGCACAGG 59.483 41.667 0.00 3.67 0.00 4.00
4247 5312 6.759497 AATAACTAAATGTGGCACTTCTCC 57.241 37.500 19.83 0.00 0.00 3.71
4255 5320 0.843309 TGGCACTTCTCCAAGGTTGA 59.157 50.000 0.00 0.00 33.37 3.18
4262 5327 1.722034 TCTCCAAGGTTGAGAGCAGT 58.278 50.000 0.00 0.00 0.00 4.40
4337 5402 9.042008 AGACAAATTAATATGTCCACATCGTAC 57.958 33.333 4.70 0.00 45.55 3.67
4369 5434 7.981102 ATTCACATCATATCAAGACATGAGG 57.019 36.000 0.00 1.86 42.53 3.86
4375 5440 8.366401 ACATCATATCAAGACATGAGGACTTAG 58.634 37.037 9.63 0.00 42.53 2.18
4426 5574 4.153117 CCTGACAAATGAACTGCTCAGTAC 59.847 45.833 2.62 0.00 41.58 2.73
4446 5620 1.501654 AACAGGAAAGAGCCCCCTCC 61.502 60.000 0.00 0.00 38.96 4.30
4469 5643 5.097742 TCAAGAAGAGAACAACAGGTTGA 57.902 39.130 18.28 0.00 42.93 3.18
4521 5709 0.679505 ACAGGCTCACAGCTAACGAA 59.320 50.000 0.00 0.00 41.99 3.85
4523 5711 0.679505 AGGCTCACAGCTAACGAACA 59.320 50.000 0.00 0.00 41.99 3.18
4529 5717 4.201628 GCTCACAGCTAACGAACATTACAG 60.202 45.833 0.00 0.00 38.45 2.74
4644 5842 2.158449 GTCAACTGTTCTGATTCTGCCG 59.842 50.000 0.00 0.00 0.00 5.69
4645 5843 2.037121 TCAACTGTTCTGATTCTGCCGA 59.963 45.455 0.00 0.00 0.00 5.54
4663 5861 2.224042 CCGAGCTGACATGTTAGCCATA 60.224 50.000 32.14 0.47 42.42 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.202566 GCGTCTAAGGCTGATGGTAAC 58.797 52.381 0.00 0.00 0.00 2.50
7 8 1.828595 TGCGTCTAAGGCTGATGGTAA 59.171 47.619 0.00 0.00 0.00 2.85
8 9 1.136305 GTGCGTCTAAGGCTGATGGTA 59.864 52.381 0.00 0.00 0.00 3.25
9 10 0.108138 GTGCGTCTAAGGCTGATGGT 60.108 55.000 0.00 0.00 0.00 3.55
10 11 0.108186 TGTGCGTCTAAGGCTGATGG 60.108 55.000 0.00 0.00 0.00 3.51
11 12 1.284657 CTGTGCGTCTAAGGCTGATG 58.715 55.000 0.00 0.00 0.00 3.07
12 13 0.898320 ACTGTGCGTCTAAGGCTGAT 59.102 50.000 0.00 0.00 0.00 2.90
13 14 0.679505 AACTGTGCGTCTAAGGCTGA 59.320 50.000 0.00 0.00 0.00 4.26
14 15 1.071605 GAACTGTGCGTCTAAGGCTG 58.928 55.000 0.00 0.00 0.00 4.85
15 16 0.037232 GGAACTGTGCGTCTAAGGCT 60.037 55.000 0.00 0.00 0.00 4.58
16 17 1.352156 CGGAACTGTGCGTCTAAGGC 61.352 60.000 0.00 0.00 33.27 4.35
17 18 0.736325 CCGGAACTGTGCGTCTAAGG 60.736 60.000 0.00 0.00 36.76 2.69
18 19 0.242825 TCCGGAACTGTGCGTCTAAG 59.757 55.000 0.00 0.00 36.76 2.18
19 20 0.038892 GTCCGGAACTGTGCGTCTAA 60.039 55.000 5.23 0.00 36.76 2.10
20 21 1.582968 GTCCGGAACTGTGCGTCTA 59.417 57.895 5.23 0.00 36.76 2.59
21 22 2.338984 GTCCGGAACTGTGCGTCT 59.661 61.111 5.23 0.00 36.76 4.18
22 23 2.737376 GGTCCGGAACTGTGCGTC 60.737 66.667 13.76 0.00 36.76 5.19
23 24 4.309950 GGGTCCGGAACTGTGCGT 62.310 66.667 21.19 0.00 36.76 5.24
25 26 4.717313 GGGGGTCCGGAACTGTGC 62.717 72.222 21.19 1.50 0.00 4.57
26 27 1.611261 TAGGGGGTCCGGAACTGTG 60.611 63.158 21.19 0.00 38.33 3.66
27 28 1.611556 GTAGGGGGTCCGGAACTGT 60.612 63.158 21.19 6.74 38.33 3.55
28 29 2.364780 GGTAGGGGGTCCGGAACTG 61.365 68.421 21.19 0.00 38.33 3.16
29 30 2.040114 GGTAGGGGGTCCGGAACT 59.960 66.667 21.19 11.67 38.33 3.01
30 31 3.085947 GGGTAGGGGGTCCGGAAC 61.086 72.222 12.37 12.37 38.33 3.62
31 32 4.783501 CGGGTAGGGGGTCCGGAA 62.784 72.222 5.23 0.00 40.07 4.30
34 35 3.447933 ATCTCGGGTAGGGGGTCCG 62.448 68.421 0.00 0.00 44.59 4.79
35 36 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
36 37 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
37 38 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
38 39 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
39 40 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
40 41 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
41 42 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
42 43 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
47 48 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
48 49 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
49 50 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
50 51 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
51 52 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
52 53 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
58 59 3.672241 GCCATTATGTCGGTGTCAAAACC 60.672 47.826 0.00 0.00 36.82 3.27
59 60 3.498082 GCCATTATGTCGGTGTCAAAAC 58.502 45.455 0.00 0.00 0.00 2.43
60 61 2.490115 GGCCATTATGTCGGTGTCAAAA 59.510 45.455 0.00 0.00 0.00 2.44
61 62 2.088423 GGCCATTATGTCGGTGTCAAA 58.912 47.619 0.00 0.00 0.00 2.69
62 63 1.680555 GGGCCATTATGTCGGTGTCAA 60.681 52.381 4.39 0.00 0.00 3.18
63 64 0.107410 GGGCCATTATGTCGGTGTCA 60.107 55.000 4.39 0.00 0.00 3.58
64 65 0.180406 AGGGCCATTATGTCGGTGTC 59.820 55.000 6.18 0.00 0.00 3.67
65 66 1.140252 GTAGGGCCATTATGTCGGTGT 59.860 52.381 6.18 0.00 0.00 4.16
66 67 1.416401 AGTAGGGCCATTATGTCGGTG 59.584 52.381 6.18 0.00 0.00 4.94
67 68 1.416401 CAGTAGGGCCATTATGTCGGT 59.584 52.381 6.18 0.00 0.00 4.69
68 69 1.270839 CCAGTAGGGCCATTATGTCGG 60.271 57.143 6.18 0.00 0.00 4.79
69 70 1.691976 TCCAGTAGGGCCATTATGTCG 59.308 52.381 6.18 0.00 36.21 4.35
70 71 3.127425 GTCCAGTAGGGCCATTATGTC 57.873 52.381 6.18 0.00 36.21 3.06
86 87 3.555324 TTCTGGTGCGCTGGTCCA 61.555 61.111 9.73 11.16 0.00 4.02
101 102 6.154445 TCTTCATCGGTAGTAGTTGTTGTTC 58.846 40.000 0.00 0.00 0.00 3.18
105 106 6.585695 TTCTCTTCATCGGTAGTAGTTGTT 57.414 37.500 0.00 0.00 0.00 2.83
106 107 5.393243 GCTTCTCTTCATCGGTAGTAGTTGT 60.393 44.000 0.00 0.00 0.00 3.32
107 108 5.038033 GCTTCTCTTCATCGGTAGTAGTTG 58.962 45.833 0.00 0.00 0.00 3.16
108 109 4.201930 CGCTTCTCTTCATCGGTAGTAGTT 60.202 45.833 0.00 0.00 0.00 2.24
109 110 3.312973 CGCTTCTCTTCATCGGTAGTAGT 59.687 47.826 0.00 0.00 0.00 2.73
110 111 3.312973 ACGCTTCTCTTCATCGGTAGTAG 59.687 47.826 0.00 0.00 0.00 2.57
111 112 3.276857 ACGCTTCTCTTCATCGGTAGTA 58.723 45.455 0.00 0.00 0.00 1.82
112 113 2.093106 ACGCTTCTCTTCATCGGTAGT 58.907 47.619 0.00 0.00 0.00 2.73
113 114 2.853731 ACGCTTCTCTTCATCGGTAG 57.146 50.000 0.00 0.00 0.00 3.18
114 115 3.276857 ACTACGCTTCTCTTCATCGGTA 58.723 45.455 0.00 0.00 0.00 4.02
115 116 2.093106 ACTACGCTTCTCTTCATCGGT 58.907 47.619 0.00 0.00 0.00 4.69
124 125 2.947852 TGCTTCTGAACTACGCTTCTC 58.052 47.619 1.83 0.00 0.00 2.87
131 132 3.686726 CAGGTTGGATGCTTCTGAACTAC 59.313 47.826 11.85 0.06 0.00 2.73
135 136 2.957402 ACAGGTTGGATGCTTCTGAA 57.043 45.000 8.43 0.00 0.00 3.02
138 139 2.906389 TGTCTACAGGTTGGATGCTTCT 59.094 45.455 0.00 0.00 0.00 2.85
179 180 3.190327 TCGGTCGACATTTAACTTCGGTA 59.810 43.478 18.91 0.00 33.50 4.02
182 183 4.259690 GGATTCGGTCGACATTTAACTTCG 60.260 45.833 18.91 8.27 0.00 3.79
189 190 2.093181 TCATGGGATTCGGTCGACATTT 60.093 45.455 18.91 0.00 0.00 2.32
192 193 0.459899 CTCATGGGATTCGGTCGACA 59.540 55.000 18.91 0.00 0.00 4.35
207 208 3.118956 GGTTTGTCTCCGACAGATCTCAT 60.119 47.826 0.00 0.00 43.69 2.90
251 252 2.002586 CCATCACAACGGTGCTTCTAG 58.997 52.381 0.00 0.00 44.87 2.43
263 264 2.124736 GCCTAGCGCCCATCACAA 60.125 61.111 2.29 0.00 0.00 3.33
274 275 1.069258 AAGGTTATCGCCGCCTAGC 59.931 57.895 0.00 0.00 31.43 3.42
283 284 7.806690 TCTTTGAAGATGAAACAAGGTTATCG 58.193 34.615 0.00 0.00 0.00 2.92
303 304 0.962356 AAGGTGATGGCGGCTCTTTG 60.962 55.000 11.43 0.00 0.00 2.77
311 312 0.534412 AGAGAGACAAGGTGATGGCG 59.466 55.000 0.00 0.00 31.91 5.69
318 319 2.630580 GTCCTGTTCAGAGAGACAAGGT 59.369 50.000 1.00 0.00 0.00 3.50
319 320 2.630098 TGTCCTGTTCAGAGAGACAAGG 59.370 50.000 1.00 0.00 0.00 3.61
324 325 4.442706 GTTTTGTGTCCTGTTCAGAGAGA 58.557 43.478 1.00 0.00 0.00 3.10
330 331 4.590918 TGTTAGGTTTTGTGTCCTGTTCA 58.409 39.130 0.00 0.00 35.51 3.18
333 334 5.479027 AGTTTTGTTAGGTTTTGTGTCCTGT 59.521 36.000 0.00 0.00 35.51 4.00
336 337 5.956642 TGAGTTTTGTTAGGTTTTGTGTCC 58.043 37.500 0.00 0.00 0.00 4.02
339 340 8.432359 GTTTCTTGAGTTTTGTTAGGTTTTGTG 58.568 33.333 0.00 0.00 0.00 3.33
345 346 6.040504 GGATGGTTTCTTGAGTTTTGTTAGGT 59.959 38.462 0.00 0.00 0.00 3.08
356 357 7.118245 GGCTTTATTTTTGGATGGTTTCTTGAG 59.882 37.037 0.00 0.00 0.00 3.02
360 361 5.547666 AGGGCTTTATTTTTGGATGGTTTCT 59.452 36.000 0.00 0.00 0.00 2.52
361 362 5.804639 AGGGCTTTATTTTTGGATGGTTTC 58.195 37.500 0.00 0.00 0.00 2.78
365 366 3.134623 GGGAGGGCTTTATTTTTGGATGG 59.865 47.826 0.00 0.00 0.00 3.51
381 382 3.849951 CACGGTGGATCGGGAGGG 61.850 72.222 0.00 0.00 35.20 4.30
387 388 3.284336 TGGAGACACGGTGGATCG 58.716 61.111 13.48 0.00 33.40 3.69
399 415 6.373759 TCTTGTAGTATTAGAGCCATGGAGA 58.626 40.000 18.40 0.37 0.00 3.71
408 424 7.517614 TGCCTCATCTCTTGTAGTATTAGAG 57.482 40.000 0.00 0.00 37.37 2.43
409 425 9.015367 GTATGCCTCATCTCTTGTAGTATTAGA 57.985 37.037 0.00 0.00 0.00 2.10
414 430 4.519350 CGGTATGCCTCATCTCTTGTAGTA 59.481 45.833 0.00 0.00 0.00 1.82
433 449 3.627952 TTTCCTGTGCCGCCGGTA 61.628 61.111 4.45 0.00 0.00 4.02
438 454 3.670377 GTGGGTTTCCTGTGCCGC 61.670 66.667 0.00 0.00 0.00 6.53
441 457 4.025401 CGCGTGGGTTTCCTGTGC 62.025 66.667 0.00 0.00 0.00 4.57
459 475 2.281900 TACACAAAGGCACCCCGC 60.282 61.111 0.00 0.00 41.28 6.13
464 480 0.941542 TCGCTTGTACACAAAGGCAC 59.058 50.000 0.00 0.00 35.15 5.01
469 485 1.134037 ACCCCTTCGCTTGTACACAAA 60.134 47.619 0.00 0.00 35.15 2.83
473 489 1.547372 GAGTACCCCTTCGCTTGTACA 59.453 52.381 0.00 0.00 36.81 2.90
478 494 2.242882 TAAGGAGTACCCCTTCGCTT 57.757 50.000 12.59 1.32 44.88 4.68
487 503 7.147949 TGCACTGACTAAGTATTAAGGAGTACC 60.148 40.741 0.00 0.00 36.83 3.34
517 533 9.990360 TCCGCATGTATTAAGAGATTTAATGTA 57.010 29.630 0.00 0.00 0.00 2.29
541 557 5.529060 AGCATGACGGAAGATTTATCTTTCC 59.471 40.000 6.45 8.12 46.47 3.13
594 610 7.457561 ACCAATGGCTTATTTATTTTGTTGGT 58.542 30.769 0.00 0.00 40.34 3.67
648 901 5.144832 TGGGACGAATGGAGTAGATATCAA 58.855 41.667 5.32 0.00 0.00 2.57
649 902 4.736473 TGGGACGAATGGAGTAGATATCA 58.264 43.478 5.32 0.00 0.00 2.15
650 903 5.923733 ATGGGACGAATGGAGTAGATATC 57.076 43.478 0.00 0.00 0.00 1.63
654 907 4.899457 ACATTATGGGACGAATGGAGTAGA 59.101 41.667 0.00 0.00 38.22 2.59
662 915 8.519799 AAAACATCTTACATTATGGGACGAAT 57.480 30.769 0.00 0.00 0.00 3.34
680 933 7.772332 ACTCCGTCTCATAATGTAAAACATC 57.228 36.000 0.00 0.00 37.97 3.06
708 961 8.871686 ACCGGCTTGAATGAATTTAATTTATC 57.128 30.769 0.00 0.00 0.00 1.75
730 983 2.169832 TCAGCTCTTTTCCTCAACCG 57.830 50.000 0.00 0.00 0.00 4.44
761 1014 9.628500 GAGGTTTATTGGATCTTGTATAGGTTT 57.372 33.333 0.00 0.00 0.00 3.27
764 1017 9.799106 AATGAGGTTTATTGGATCTTGTATAGG 57.201 33.333 0.00 0.00 0.00 2.57
767 1020 9.927081 AGAAATGAGGTTTATTGGATCTTGTAT 57.073 29.630 0.00 0.00 0.00 2.29
787 1040 5.419239 ACAGAGGGAGAGAGAAAGAAATG 57.581 43.478 0.00 0.00 0.00 2.32
817 1074 4.651503 CCTCTCTCTCTCTCTCTCTAGTGT 59.348 50.000 0.00 0.00 0.00 3.55
830 1087 2.357777 GGCCAACTACTCCTCTCTCTCT 60.358 54.545 0.00 0.00 0.00 3.10
831 1088 2.028876 GGCCAACTACTCCTCTCTCTC 58.971 57.143 0.00 0.00 0.00 3.20
832 1089 1.359474 TGGCCAACTACTCCTCTCTCT 59.641 52.381 0.61 0.00 0.00 3.10
834 1091 2.327325 TTGGCCAACTACTCCTCTCT 57.673 50.000 16.05 0.00 0.00 3.10
835 1092 2.158885 GGATTGGCCAACTACTCCTCTC 60.159 54.545 23.27 10.94 36.34 3.20
836 1093 1.840635 GGATTGGCCAACTACTCCTCT 59.159 52.381 23.27 0.01 36.34 3.69
837 1094 1.473434 CGGATTGGCCAACTACTCCTC 60.473 57.143 26.07 16.62 35.94 3.71
838 1095 0.541863 CGGATTGGCCAACTACTCCT 59.458 55.000 26.07 9.43 35.94 3.69
839 1096 0.463833 CCGGATTGGCCAACTACTCC 60.464 60.000 23.27 22.13 35.94 3.85
840 1097 0.539986 TCCGGATTGGCCAACTACTC 59.460 55.000 23.27 14.55 37.80 2.59
841 1098 0.252197 GTCCGGATTGGCCAACTACT 59.748 55.000 23.27 4.19 37.80 2.57
842 1099 0.035820 TGTCCGGATTGGCCAACTAC 60.036 55.000 23.27 15.01 37.80 2.73
843 1100 0.693622 TTGTCCGGATTGGCCAACTA 59.306 50.000 23.27 0.00 37.80 2.24
1329 1616 4.560128 GCGTCTGAATCAGGCAATATCTA 58.440 43.478 15.64 0.00 35.60 1.98
1346 1633 1.429463 GTCCTCAACAATTCGCGTCT 58.571 50.000 5.77 0.00 0.00 4.18
1394 1682 2.562298 TGTTCCACCATTCCATCAAAGC 59.438 45.455 0.00 0.00 0.00 3.51
1407 1695 0.679960 GGTGCTACCCATGTTCCACC 60.680 60.000 0.00 0.00 37.30 4.61
1427 1715 1.347221 CGATTAAGGTCAACGGCGC 59.653 57.895 6.90 0.00 0.00 6.53
1459 1747 2.101415 AGTTTTGCTGACTGGAAAAGGC 59.899 45.455 11.15 2.78 44.50 4.35
1517 1805 6.867662 AAAAATCTCTGAAACATCTCACGT 57.132 33.333 0.00 0.00 0.00 4.49
1541 1829 1.819288 CCAGAGCTAGTTCACCGAAGA 59.181 52.381 9.43 0.00 0.00 2.87
1542 1830 1.134965 CCCAGAGCTAGTTCACCGAAG 60.135 57.143 9.43 0.00 0.00 3.79
1573 1862 6.150396 AGCTACACCAATCTCTGTATACAC 57.850 41.667 0.08 0.00 0.00 2.90
1606 1895 6.751514 TCACTAAGACAAAACAAGCAAGAA 57.248 33.333 0.00 0.00 0.00 2.52
1632 1921 3.319972 CACCAAGGCATATTCTGAATGGG 59.680 47.826 13.01 6.04 31.36 4.00
1633 1922 3.319972 CCACCAAGGCATATTCTGAATGG 59.680 47.826 13.01 7.65 32.61 3.16
1634 1923 4.209538 TCCACCAAGGCATATTCTGAATG 58.790 43.478 13.01 0.00 37.29 2.67
1635 1924 4.524802 TCCACCAAGGCATATTCTGAAT 57.475 40.909 8.14 8.14 37.29 2.57
1636 1925 4.314522 TTCCACCAAGGCATATTCTGAA 57.685 40.909 0.00 0.00 37.29 3.02
1647 1936 3.070015 AGCAACTCAAATTTCCACCAAGG 59.930 43.478 0.00 0.00 39.47 3.61
1680 2018 5.305902 TGGAATTTTTCTCCCACCCTAAAAC 59.694 40.000 0.00 0.00 31.32 2.43
2030 2369 0.659957 GCGATGTCAATGCTTCCCTC 59.340 55.000 0.00 0.00 0.00 4.30
2050 2389 3.118956 GGACATCTTTCATCGAGTGGACT 60.119 47.826 0.00 0.00 0.00 3.85
2438 2873 3.758554 ACATAAGGGACATGAAACAGCAC 59.241 43.478 0.00 0.00 0.00 4.40
2441 2876 3.129287 GGCACATAAGGGACATGAAACAG 59.871 47.826 0.00 0.00 0.00 3.16
2452 2887 2.418368 TACTGCTTGGCACATAAGGG 57.582 50.000 0.00 0.00 39.30 3.95
2731 3171 1.401761 TGTTGCAGTTTCTGGCATGT 58.598 45.000 0.00 0.00 40.17 3.21
2960 3400 6.150641 CCTATCAATTTATCAGAGGCACATGG 59.849 42.308 0.00 0.00 0.00 3.66
3020 3460 4.500127 TGGTAAGAACATGATGTGGTACG 58.500 43.478 0.00 0.00 0.00 3.67
3337 3964 4.347583 AGAGGGAGGATCAGCATCTTTAAG 59.652 45.833 0.00 0.00 36.25 1.85
3447 4075 4.153117 GCAGTTACCATCAAGAACAGACAG 59.847 45.833 0.00 0.00 0.00 3.51
3738 4390 1.494721 TCAAAGAAACCAGGTCCAGCT 59.505 47.619 0.00 0.00 0.00 4.24
3896 4549 1.135199 TGTTCTAAGCTCTAACCCGCG 60.135 52.381 0.00 0.00 0.00 6.46
3907 4560 1.798813 CCACTGAACCGTGTTCTAAGC 59.201 52.381 14.95 0.00 33.07 3.09
3922 4575 5.070001 TCCAGAAAGGATAACAAACCACTG 58.930 41.667 0.00 0.00 43.07 3.66
4036 4704 3.441496 ACAACATTGGCAAACAGTGAG 57.559 42.857 3.01 3.45 38.97 3.51
4039 4707 7.622893 AAAATAAACAACATTGGCAAACAGT 57.377 28.000 3.01 0.26 0.00 3.55
4073 4741 6.214191 AGATATGATCGGTATTAGCACAGG 57.786 41.667 0.00 0.00 0.00 4.00
4247 5312 2.693069 CTACCACTGCTCTCAACCTTG 58.307 52.381 0.00 0.00 0.00 3.61
4255 5320 1.339438 CCAATGTGCTACCACTGCTCT 60.339 52.381 0.00 0.00 42.54 4.09
4262 5327 2.869101 TAACTGCCAATGTGCTACCA 57.131 45.000 0.00 0.00 0.00 3.25
4311 5376 9.042008 GTACGATGTGGACATATTAATTTGTCT 57.958 33.333 27.38 14.92 41.55 3.41
4317 5382 8.201464 TGTCTTGTACGATGTGGACATATTAAT 58.799 33.333 0.00 0.00 36.57 1.40
4337 5402 9.499585 GTCTTGATATGATGTGAATTTGTCTTG 57.500 33.333 0.00 0.00 0.00 3.02
4426 5574 0.322906 GAGGGGGCTCTTTCCTGTTG 60.323 60.000 0.00 0.00 0.00 3.33
4446 5620 5.007136 GTCAACCTGTTGTTCTCTTCTTGAG 59.993 44.000 9.65 0.00 41.28 3.02
4469 5643 7.604164 CAGGTTAAGATTATCAGTCTGTGTTGT 59.396 37.037 0.00 0.00 0.00 3.32
4510 5698 4.689345 GGAACTGTAATGTTCGTTAGCTGT 59.311 41.667 0.00 0.00 45.11 4.40
4521 5709 5.833131 ACTTGGAATGTTGGAACTGTAATGT 59.167 36.000 0.00 0.00 0.00 2.71
4523 5711 6.549364 TGAACTTGGAATGTTGGAACTGTAAT 59.451 34.615 0.00 0.00 34.00 1.89
4529 5717 4.475944 CGATGAACTTGGAATGTTGGAAC 58.524 43.478 0.00 0.00 34.00 3.62
4644 5842 4.892433 AGATATGGCTAACATGTCAGCTC 58.108 43.478 20.36 10.09 46.63 4.09
4645 5843 4.970860 AGATATGGCTAACATGTCAGCT 57.029 40.909 20.36 4.46 46.63 4.24
4663 5861 0.982704 AGCCAGTGACTGCTGAAGAT 59.017 50.000 7.16 0.00 38.70 2.40


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

AutoCloner maintained by Alex Coulton.