Multiple sequence alignment - TraesCS1A01G269300

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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 TraesCS1A01G269300 chr1A 100.000 3644 0 0 1 3644 463920287 463923930 0.000000e+00 6730
1 TraesCS1A01G269300 chr1A 87.000 200 26 0 3445 3644 463930074 463930273 3.660000e-55 226
2 TraesCS1A01G269300 chr1D 92.602 2825 114 43 850 3644 365040533 365043292 0.000000e+00 3971
3 TraesCS1A01G269300 chr1D 89.213 445 29 12 389 828 365040007 365040437 4.140000e-149 538
4 TraesCS1A01G269300 chr1D 86.567 201 27 0 3444 3644 365063791 365063991 4.740000e-54 222
5 TraesCS1A01G269300 chr1B 92.001 2838 117 47 851 3644 488393328 488396099 0.000000e+00 3882
6 TraesCS1A01G269300 chr1B 88.701 354 26 11 473 825 488392875 488393215 1.560000e-113 420
7 TraesCS1A01G269300 chr1B 83.193 357 44 11 72 427 488392519 488392860 2.730000e-81 313
8 TraesCS1A01G269300 chr1B 89.552 201 21 0 3444 3644 488463850 488464050 4.670000e-64 255
9 TraesCS1A01G269300 chr1B 100.000 66 0 0 1 66 488373865 488373930 4.940000e-24 122
10 TraesCS1A01G269300 chr3A 86.149 1379 173 17 1228 2597 632777601 632776232 0.000000e+00 1472
11 TraesCS1A01G269300 chr3A 80.335 478 81 9 1 475 491453413 491453880 2.080000e-92 350
12 TraesCS1A01G269300 chr3B 85.839 1377 181 14 1228 2597 652497352 652495983 0.000000e+00 1450
13 TraesCS1A01G269300 chr3D 85.204 1399 187 19 1209 2597 490305334 490303946 0.000000e+00 1419


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 TraesCS1A01G269300 chr1A 463920287 463923930 3643 False 6730.000000 6730 100.0000 1 3644 1 chr1A.!!$F1 3643
1 TraesCS1A01G269300 chr1D 365040007 365043292 3285 False 2254.500000 3971 90.9075 389 3644 2 chr1D.!!$F2 3255
2 TraesCS1A01G269300 chr1B 488392519 488396099 3580 False 1538.333333 3882 87.9650 72 3644 3 chr1B.!!$F3 3572
3 TraesCS1A01G269300 chr3A 632776232 632777601 1369 True 1472.000000 1472 86.1490 1228 2597 1 chr3A.!!$R1 1369
4 TraesCS1A01G269300 chr3B 652495983 652497352 1369 True 1450.000000 1450 85.8390 1228 2597 1 chr3B.!!$R1 1369
5 TraesCS1A01G269300 chr3D 490303946 490305334 1388 True 1419.000000 1419 85.2040 1209 2597 1 chr3D.!!$R1 1388

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
203 204 0.037605 GTCTCGATGGGTTCCGTTGT 60.038 55.0 0.0 0.0 0.0 3.32 F
502 508 0.101759 CCAGCATCAGGATTTTGGCG 59.898 55.0 0.0 0.0 0.0 5.69 F
846 874 0.833287 CCCCACCACTCAGTATCAGG 59.167 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1708 0.321564 TGGTGTTGAAGATGGAGCCG 60.322 55.0 0.00 0.0 0.0 5.52 R
2103 2203 0.832135 AGAAGCCAGAGTCGGGAACA 60.832 55.0 14.12 0.0 0.0 3.18 R
2756 2876 0.245539 CAAGCATGCCCAGGTTTCAG 59.754 55.0 15.66 0.0 0.0 3.02 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 2.134201 GCAACTGCTTTGGTGGTTAC 57.866 50.000 0.00 0.00 38.21 2.50
21 22 1.681264 GCAACTGCTTTGGTGGTTACT 59.319 47.619 0.00 0.00 38.21 2.24
22 23 2.882137 GCAACTGCTTTGGTGGTTACTA 59.118 45.455 0.00 0.00 38.21 1.82
23 24 3.506067 GCAACTGCTTTGGTGGTTACTAT 59.494 43.478 0.00 0.00 38.21 2.12
24 25 4.022329 GCAACTGCTTTGGTGGTTACTATT 60.022 41.667 0.00 0.00 38.21 1.73
25 26 5.508994 GCAACTGCTTTGGTGGTTACTATTT 60.509 40.000 0.00 0.00 38.21 1.40
26 27 5.705609 ACTGCTTTGGTGGTTACTATTTG 57.294 39.130 0.00 0.00 0.00 2.32
27 28 4.522789 ACTGCTTTGGTGGTTACTATTTGG 59.477 41.667 0.00 0.00 0.00 3.28
28 29 3.257127 TGCTTTGGTGGTTACTATTTGGC 59.743 43.478 0.00 0.00 0.00 4.52
29 30 3.257127 GCTTTGGTGGTTACTATTTGGCA 59.743 43.478 0.00 0.00 0.00 4.92
30 31 4.805219 CTTTGGTGGTTACTATTTGGCAC 58.195 43.478 0.00 0.00 0.00 5.01
31 32 3.510531 TGGTGGTTACTATTTGGCACA 57.489 42.857 0.00 0.00 0.00 4.57
32 33 4.040936 TGGTGGTTACTATTTGGCACAT 57.959 40.909 0.00 0.00 39.30 3.21
33 34 4.411927 TGGTGGTTACTATTTGGCACATT 58.588 39.130 0.00 0.00 39.30 2.71
34 35 4.835615 TGGTGGTTACTATTTGGCACATTT 59.164 37.500 0.00 0.00 39.30 2.32
35 36 5.167845 GGTGGTTACTATTTGGCACATTTG 58.832 41.667 0.00 0.00 39.30 2.32
36 37 5.167845 GTGGTTACTATTTGGCACATTTGG 58.832 41.667 0.00 0.00 39.30 3.28
37 38 4.221703 TGGTTACTATTTGGCACATTTGGG 59.778 41.667 0.00 0.00 39.30 4.12
38 39 4.464597 GGTTACTATTTGGCACATTTGGGA 59.535 41.667 0.00 0.00 39.30 4.37
39 40 5.394115 GGTTACTATTTGGCACATTTGGGAG 60.394 44.000 0.00 0.00 39.30 4.30
40 41 3.099141 ACTATTTGGCACATTTGGGAGG 58.901 45.455 0.00 0.00 39.30 4.30
41 42 0.614812 ATTTGGCACATTTGGGAGGC 59.385 50.000 0.00 0.00 39.30 4.70
42 43 1.814772 TTTGGCACATTTGGGAGGCG 61.815 55.000 0.00 0.00 39.30 5.52
43 44 2.361104 GGCACATTTGGGAGGCGA 60.361 61.111 0.00 0.00 0.00 5.54
44 45 2.409870 GGCACATTTGGGAGGCGAG 61.410 63.158 0.00 0.00 0.00 5.03
45 46 2.409870 GCACATTTGGGAGGCGAGG 61.410 63.158 0.00 0.00 0.00 4.63
46 47 1.299648 CACATTTGGGAGGCGAGGA 59.700 57.895 0.00 0.00 0.00 3.71
47 48 0.322456 CACATTTGGGAGGCGAGGAA 60.322 55.000 0.00 0.00 0.00 3.36
48 49 0.625849 ACATTTGGGAGGCGAGGAAT 59.374 50.000 0.00 0.00 0.00 3.01
49 50 1.027357 CATTTGGGAGGCGAGGAATG 58.973 55.000 0.00 0.00 0.00 2.67
50 51 0.918983 ATTTGGGAGGCGAGGAATGA 59.081 50.000 0.00 0.00 0.00 2.57
51 52 0.918983 TTTGGGAGGCGAGGAATGAT 59.081 50.000 0.00 0.00 0.00 2.45
52 53 0.181114 TTGGGAGGCGAGGAATGATG 59.819 55.000 0.00 0.00 0.00 3.07
53 54 0.982852 TGGGAGGCGAGGAATGATGT 60.983 55.000 0.00 0.00 0.00 3.06
54 55 0.250081 GGGAGGCGAGGAATGATGTC 60.250 60.000 0.00 0.00 0.00 3.06
55 56 0.465705 GGAGGCGAGGAATGATGTCA 59.534 55.000 0.00 0.00 0.00 3.58
56 57 1.539929 GGAGGCGAGGAATGATGTCAG 60.540 57.143 0.00 0.00 0.00 3.51
57 58 0.467384 AGGCGAGGAATGATGTCAGG 59.533 55.000 0.00 0.00 0.00 3.86
58 59 0.465705 GGCGAGGAATGATGTCAGGA 59.534 55.000 0.00 0.00 0.00 3.86
59 60 1.134401 GGCGAGGAATGATGTCAGGAA 60.134 52.381 0.00 0.00 0.00 3.36
60 61 1.936547 GCGAGGAATGATGTCAGGAAC 59.063 52.381 0.00 0.00 0.00 3.62
61 62 2.677902 GCGAGGAATGATGTCAGGAACA 60.678 50.000 0.00 0.00 43.51 3.18
62 63 3.599343 CGAGGAATGATGTCAGGAACAA 58.401 45.455 0.00 0.00 42.37 2.83
63 64 4.194640 CGAGGAATGATGTCAGGAACAAT 58.805 43.478 0.00 0.00 42.37 2.71
64 65 4.034858 CGAGGAATGATGTCAGGAACAATG 59.965 45.833 0.00 0.00 42.37 2.82
65 66 4.275810 AGGAATGATGTCAGGAACAATGG 58.724 43.478 0.00 0.00 42.37 3.16
66 67 4.019174 GGAATGATGTCAGGAACAATGGT 58.981 43.478 0.00 0.00 42.37 3.55
67 68 4.142315 GGAATGATGTCAGGAACAATGGTG 60.142 45.833 0.00 0.00 42.37 4.17
68 69 2.161855 TGATGTCAGGAACAATGGTGC 58.838 47.619 0.00 0.00 42.37 5.01
69 70 1.131126 GATGTCAGGAACAATGGTGCG 59.869 52.381 0.00 0.00 42.37 5.34
70 71 0.888736 TGTCAGGAACAATGGTGCGG 60.889 55.000 0.00 0.00 34.03 5.69
77 78 0.398696 AACAATGGTGCGGTCCTACA 59.601 50.000 0.00 0.00 0.00 2.74
83 84 1.327690 GGTGCGGTCCTACATCCTCA 61.328 60.000 0.00 0.00 0.00 3.86
96 97 1.613317 ATCCTCATCGTGTGGCCGAA 61.613 55.000 0.00 0.00 40.73 4.30
127 128 3.191162 TGCTTATGTGGAGTTGATTGTGC 59.809 43.478 0.00 0.00 0.00 4.57
149 150 4.915704 CAGAACTGCTTTTAAAACCGTCA 58.084 39.130 0.00 0.00 0.00 4.35
152 153 5.803461 AGAACTGCTTTTAAAACCGTCAAAC 59.197 36.000 0.00 0.00 0.00 2.93
155 156 4.674475 TGCTTTTAAAACCGTCAAACCTC 58.326 39.130 0.00 0.00 0.00 3.85
159 160 7.088272 GCTTTTAAAACCGTCAAACCTCATAT 58.912 34.615 0.00 0.00 0.00 1.78
164 165 2.945008 ACCGTCAAACCTCATATGCATG 59.055 45.455 10.16 0.00 0.00 4.06
175 176 3.023119 TCATATGCATGTCCACCCAAAC 58.977 45.455 10.16 0.00 33.57 2.93
179 180 0.831711 GCATGTCCACCCAAACCCTT 60.832 55.000 0.00 0.00 0.00 3.95
180 181 1.715785 CATGTCCACCCAAACCCTTT 58.284 50.000 0.00 0.00 0.00 3.11
197 198 2.076863 CTTTGGTGTCTCGATGGGTTC 58.923 52.381 0.00 0.00 0.00 3.62
199 200 1.153628 GGTGTCTCGATGGGTTCCG 60.154 63.158 0.00 0.00 0.00 4.30
203 204 0.037605 GTCTCGATGGGTTCCGTTGT 60.038 55.000 0.00 0.00 0.00 3.32
211 212 0.942252 GGGTTCCGTTGTCAACAGAC 59.058 55.000 15.79 9.80 0.00 3.51
213 214 1.329599 GGTTCCGTTGTCAACAGACAC 59.670 52.381 15.79 9.97 41.68 3.67
214 215 2.004017 GTTCCGTTGTCAACAGACACA 58.996 47.619 15.79 0.00 41.68 3.72
216 217 2.912771 TCCGTTGTCAACAGACACAAT 58.087 42.857 15.79 0.00 41.68 2.71
233 234 8.227119 CAGACACAATGTTCGTAAATGTTGATA 58.773 33.333 0.00 0.00 0.00 2.15
240 241 6.318628 TGTTCGTAAATGTTGATAATGCACC 58.681 36.000 0.00 0.00 0.00 5.01
241 242 6.072452 TGTTCGTAAATGTTGATAATGCACCA 60.072 34.615 0.00 0.00 0.00 4.17
256 257 1.130373 GCACCATTTCAGAATTCGCGA 59.870 47.619 3.71 3.71 0.00 5.87
257 258 2.774007 CACCATTTCAGAATTCGCGAC 58.226 47.619 9.15 0.00 0.00 5.19
258 259 1.393539 ACCATTTCAGAATTCGCGACG 59.606 47.619 9.15 0.00 0.00 5.12
263 264 0.527600 TCAGAATTCGCGACGGATGG 60.528 55.000 9.15 0.00 0.00 3.51
265 266 1.227147 GAATTCGCGACGGATGGGA 60.227 57.895 9.15 0.00 0.00 4.37
271 272 4.530857 CGACGGATGGGAGTGGGC 62.531 72.222 0.00 0.00 0.00 5.36
280 281 2.351276 GGAGTGGGCGTGGTGATT 59.649 61.111 0.00 0.00 0.00 2.57
283 284 0.605319 GAGTGGGCGTGGTGATTTGA 60.605 55.000 0.00 0.00 0.00 2.69
309 311 1.007502 GCGATTGTGCTTGTTGGCA 60.008 52.632 0.00 0.00 40.15 4.92
312 314 1.336148 CGATTGTGCTTGTTGGCATGT 60.336 47.619 0.00 0.00 44.34 3.21
315 317 0.385029 TGTGCTTGTTGGCATGTCAC 59.615 50.000 0.00 0.00 44.34 3.67
325 327 1.581912 GCATGTCACGAGCGCATTG 60.582 57.895 11.47 2.93 0.00 2.82
335 337 1.576356 GAGCGCATTGAGGAGGTTAG 58.424 55.000 11.47 0.00 0.00 2.34
341 343 2.928334 CATTGAGGAGGTTAGCATGCT 58.072 47.619 25.99 25.99 0.00 3.79
361 363 4.829064 CTAGAACTAGCTGAGGCACTAG 57.171 50.000 0.00 0.00 41.55 2.57
362 364 1.754226 AGAACTAGCTGAGGCACTAGC 59.246 52.381 0.00 0.00 41.55 3.42
363 365 0.457851 AACTAGCTGAGGCACTAGCG 59.542 55.000 0.00 0.00 41.55 4.26
364 366 1.299773 CTAGCTGAGGCACTAGCGC 60.300 63.158 0.00 0.00 41.55 5.92
365 367 1.733402 CTAGCTGAGGCACTAGCGCT 61.733 60.000 17.26 17.26 41.55 5.92
366 368 1.323271 TAGCTGAGGCACTAGCGCTT 61.323 55.000 18.68 0.00 41.55 4.68
367 369 2.170434 GCTGAGGCACTAGCGCTTC 61.170 63.158 18.68 6.37 41.55 3.86
368 370 1.875813 CTGAGGCACTAGCGCTTCG 60.876 63.158 18.68 10.39 41.55 3.79
369 371 2.271607 CTGAGGCACTAGCGCTTCGA 62.272 60.000 18.68 0.00 41.55 3.71
370 372 1.874466 GAGGCACTAGCGCTTCGAC 60.874 63.158 18.68 6.70 41.55 4.20
371 373 2.126071 GGCACTAGCGCTTCGACA 60.126 61.111 18.68 0.00 43.41 4.35
372 374 2.445438 GGCACTAGCGCTTCGACAC 61.445 63.158 18.68 0.08 43.41 3.67
373 375 2.778997 GCACTAGCGCTTCGACACG 61.779 63.158 18.68 2.00 0.00 4.49
379 381 4.409588 CGCTTCGACACGCCGTTG 62.410 66.667 0.00 0.00 0.00 4.10
380 382 4.719616 GCTTCGACACGCCGTTGC 62.720 66.667 0.00 0.00 0.00 4.17
381 383 3.036084 CTTCGACACGCCGTTGCT 61.036 61.111 0.00 0.00 34.43 3.91
382 384 3.000080 CTTCGACACGCCGTTGCTC 62.000 63.158 0.00 0.00 34.43 4.26
383 385 3.493830 TTCGACACGCCGTTGCTCT 62.494 57.895 0.00 0.00 34.43 4.09
384 386 3.470567 CGACACGCCGTTGCTCTC 61.471 66.667 0.00 0.00 34.43 3.20
385 387 2.355837 GACACGCCGTTGCTCTCA 60.356 61.111 0.00 0.00 34.43 3.27
392 394 1.444553 CCGTTGCTCTCACTCGTCC 60.445 63.158 0.00 0.00 0.00 4.79
416 418 6.660949 CCAGAAGGTTTTCATAAGGTCATCTT 59.339 38.462 0.00 0.00 36.35 2.40
430 432 4.590647 AGGTCATCTTCTTCACTTCAGACA 59.409 41.667 0.00 0.00 0.00 3.41
438 440 4.611943 TCTTCACTTCAGACAGTCTTTCG 58.388 43.478 0.00 0.00 0.00 3.46
486 492 4.639310 ACAATAGACCGTAGTAGTCACCAG 59.361 45.833 0.00 0.00 36.68 4.00
492 498 2.223595 CCGTAGTAGTCACCAGCATCAG 60.224 54.545 0.00 0.00 0.00 2.90
500 506 2.165030 GTCACCAGCATCAGGATTTTGG 59.835 50.000 7.08 7.08 0.00 3.28
502 508 0.101759 CCAGCATCAGGATTTTGGCG 59.898 55.000 0.00 0.00 0.00 5.69
547 553 8.177119 TCTTTAGTCATTGTTAGCCATTTGTT 57.823 30.769 0.00 0.00 0.00 2.83
560 566 1.000731 CATTTGTTGAATGTGGGCGGT 59.999 47.619 0.00 0.00 40.23 5.68
598 604 5.237779 TGTGTTTTTCTTCCGGTGATTCTAC 59.762 40.000 0.00 0.00 0.00 2.59
603 609 4.884668 TCTTCCGGTGATTCTACTTTGT 57.115 40.909 0.00 0.00 0.00 2.83
619 625 2.264005 TTGTGCAATGTAACTCCGGT 57.736 45.000 0.00 0.00 0.00 5.28
671 677 9.927668 AATATTTTGTGGTGAATAAAAGAGTGG 57.072 29.630 0.00 0.00 33.07 4.00
672 678 6.783708 TTTTGTGGTGAATAAAAGAGTGGT 57.216 33.333 0.00 0.00 0.00 4.16
673 679 7.883391 TTTTGTGGTGAATAAAAGAGTGGTA 57.117 32.000 0.00 0.00 0.00 3.25
674 680 8.472007 TTTTGTGGTGAATAAAAGAGTGGTAT 57.528 30.769 0.00 0.00 0.00 2.73
675 681 9.575868 TTTTGTGGTGAATAAAAGAGTGGTATA 57.424 29.630 0.00 0.00 0.00 1.47
676 682 9.747898 TTTGTGGTGAATAAAAGAGTGGTATAT 57.252 29.630 0.00 0.00 0.00 0.86
677 683 9.747898 TTGTGGTGAATAAAAGAGTGGTATATT 57.252 29.630 0.00 0.00 0.00 1.28
844 872 1.078823 AGTCCCCACCACTCAGTATCA 59.921 52.381 0.00 0.00 0.00 2.15
845 873 1.482593 GTCCCCACCACTCAGTATCAG 59.517 57.143 0.00 0.00 0.00 2.90
846 874 0.833287 CCCCACCACTCAGTATCAGG 59.167 60.000 0.00 0.00 0.00 3.86
847 875 1.573108 CCCACCACTCAGTATCAGGT 58.427 55.000 0.00 0.00 0.00 4.00
848 876 1.909302 CCCACCACTCAGTATCAGGTT 59.091 52.381 0.00 0.00 0.00 3.50
888 985 3.047877 CACGAGCCGACCAAACCC 61.048 66.667 1.50 0.00 0.00 4.11
1055 1155 4.899239 GCGCCTCCTCCATCACCG 62.899 72.222 0.00 0.00 0.00 4.94
1060 1160 3.723235 CTCCTCCATCACCGCCACG 62.723 68.421 0.00 0.00 0.00 4.94
1314 1414 1.685224 CTACCTGGGCCTGCAGAAA 59.315 57.895 17.39 0.00 0.00 2.52
1380 1480 2.720758 CGACGGCAAGCTCAAGTCG 61.721 63.158 15.73 15.73 46.32 4.18
1539 1639 4.078516 GCGGGCTACAGGTTCGGT 62.079 66.667 0.00 0.00 0.00 4.69
2103 2203 3.771160 GCCGACGTGGTCATCCCT 61.771 66.667 0.00 0.00 41.21 4.20
2251 2351 1.302033 CTGGCCGTGAAGCTCAAGT 60.302 57.895 0.00 0.00 0.00 3.16
2689 2804 1.404717 CCTCTGCATCAGCTGTAACGT 60.405 52.381 14.67 0.00 42.74 3.99
2690 2805 2.341257 CTCTGCATCAGCTGTAACGTT 58.659 47.619 14.67 5.88 42.74 3.99
2691 2806 3.511699 CTCTGCATCAGCTGTAACGTTA 58.488 45.455 14.67 3.29 42.74 3.18
2692 2807 3.511699 TCTGCATCAGCTGTAACGTTAG 58.488 45.455 14.67 0.31 42.74 2.34
2727 2842 8.845942 TTGCGAATTTTCTTAGATCATCAATG 57.154 30.769 0.00 0.00 0.00 2.82
2756 2876 2.514824 GCCCCTCCATTGCTCGAC 60.515 66.667 0.00 0.00 0.00 4.20
2766 2886 1.466167 CATTGCTCGACTGAAACCTGG 59.534 52.381 0.00 0.00 0.00 4.45
2768 2888 2.035442 GCTCGACTGAAACCTGGGC 61.035 63.158 0.00 0.00 0.00 5.36
2770 2890 0.036010 CTCGACTGAAACCTGGGCAT 60.036 55.000 0.00 0.00 0.00 4.40
2806 2926 0.037139 TGCCTGCAACATCATTTGGC 60.037 50.000 1.12 1.12 39.33 4.52
2827 2947 3.152341 CCATGAATTCTATCCCTGGTGC 58.848 50.000 7.05 0.00 0.00 5.01
2855 2975 0.311790 AGTTGCTGCAATGGTTGACG 59.688 50.000 19.11 0.00 0.00 4.35
2872 2992 3.841643 TGACGTTCGATTAAACCTCTCC 58.158 45.455 0.00 0.00 0.00 3.71
2890 3010 2.037208 AACCCCCGGGAAAGCATG 59.963 61.111 26.32 2.05 38.96 4.06
2894 3014 1.750399 CCCCGGGAAAGCATGACTG 60.750 63.158 26.32 0.00 0.00 3.51
2895 3015 1.750399 CCCGGGAAAGCATGACTGG 60.750 63.158 18.48 0.00 0.00 4.00
2897 3017 2.409870 CGGGAAAGCATGACTGGGC 61.410 63.158 0.00 0.00 0.00 5.36
2901 3021 1.941999 GAAAGCATGACTGGGCAGGC 61.942 60.000 4.82 4.82 45.16 4.85
2902 3022 3.951769 AAGCATGACTGGGCAGGCC 62.952 63.158 9.53 5.91 45.90 5.19
2903 3023 4.437587 GCATGACTGGGCAGGCCT 62.438 66.667 15.38 0.00 39.47 5.19
2904 3024 2.439701 CATGACTGGGCAGGCCTG 60.440 66.667 29.34 29.34 34.90 4.85
2905 3025 2.611800 ATGACTGGGCAGGCCTGA 60.612 61.111 37.21 15.06 34.90 3.86
2941 3094 1.327303 TTGCCAACACTGAATCCACC 58.673 50.000 0.00 0.00 0.00 4.61
2970 3123 4.862641 ACACCCAGTTAAAGGCATCTAT 57.137 40.909 0.00 0.00 0.00 1.98
2971 3124 4.781934 ACACCCAGTTAAAGGCATCTATC 58.218 43.478 0.00 0.00 0.00 2.08
2973 3126 5.665812 ACACCCAGTTAAAGGCATCTATCTA 59.334 40.000 0.00 0.00 0.00 1.98
2975 3128 7.054124 CACCCAGTTAAAGGCATCTATCTAAA 58.946 38.462 0.00 0.00 0.00 1.85
2976 3129 7.721399 CACCCAGTTAAAGGCATCTATCTAAAT 59.279 37.037 0.00 0.00 0.00 1.40
2977 3130 8.282256 ACCCAGTTAAAGGCATCTATCTAAATT 58.718 33.333 0.00 0.00 0.00 1.82
2978 3131 8.571336 CCCAGTTAAAGGCATCTATCTAAATTG 58.429 37.037 0.00 0.00 0.00 2.32
3021 3174 6.366061 ACACTTTCAGCAAACTTTTCTGAAAC 59.634 34.615 19.34 0.00 46.01 2.78
3022 3175 5.572896 ACTTTCAGCAAACTTTTCTGAAACG 59.427 36.000 19.34 17.29 46.01 3.60
3029 3182 0.110823 CTTTTCTGAAACGGGTCGCG 60.111 55.000 7.88 7.88 0.00 5.87
3032 3185 0.530211 TTCTGAAACGGGTCGCGAAA 60.530 50.000 12.06 0.00 0.00 3.46
3121 3302 2.404215 TCAGCTACGACTTTGAACTGC 58.596 47.619 0.00 0.00 0.00 4.40
3145 3326 1.804748 GTCGGTGCTAAAACCCAAGAG 59.195 52.381 0.00 0.00 36.84 2.85
3155 3336 6.016276 TGCTAAAACCCAAGAGTCAAGAATTC 60.016 38.462 0.00 0.00 0.00 2.17
3173 3354 9.298250 CAAGAATTCAGGATGGATGAATCTATT 57.702 33.333 8.44 0.00 44.57 1.73
3237 3418 1.835483 GCTATGCGCCCATGTTCTCG 61.835 60.000 4.18 0.00 32.85 4.04
3273 3462 1.129437 GAAGAAGAGCAATGCCGTGTC 59.871 52.381 0.00 0.00 0.00 3.67
3293 3482 0.947244 CAAGTGTGTCTGTGCTTCCC 59.053 55.000 0.00 0.00 0.00 3.97
3296 3485 1.620819 AGTGTGTCTGTGCTTCCCTAG 59.379 52.381 0.00 0.00 0.00 3.02
3299 3488 2.561419 TGTGTCTGTGCTTCCCTAGTAC 59.439 50.000 0.00 0.00 39.65 2.73
3300 3489 2.826725 GTGTCTGTGCTTCCCTAGTACT 59.173 50.000 0.00 0.00 39.88 2.73
3301 3490 2.826128 TGTCTGTGCTTCCCTAGTACTG 59.174 50.000 5.39 0.00 39.88 2.74
3318 3507 8.744652 CCTAGTACTGTAAGCTCATAGCAATAT 58.255 37.037 5.39 0.00 45.56 1.28
3351 3543 6.673154 AAGTAAAACTGAAACGTTACTGCT 57.327 33.333 0.00 0.00 36.99 4.24
3379 3572 5.587844 AGAATCAGCACATGAATAGTGGAAC 59.412 40.000 0.00 0.00 42.53 3.62
3393 3586 1.927487 TGGAACTGCCAGCATTGAAT 58.073 45.000 0.00 0.00 43.33 2.57
3394 3587 3.084536 TGGAACTGCCAGCATTGAATA 57.915 42.857 0.00 0.00 43.33 1.75
3395 3588 3.018856 TGGAACTGCCAGCATTGAATAG 58.981 45.455 0.00 0.00 43.33 1.73
3396 3589 3.019564 GGAACTGCCAGCATTGAATAGT 58.980 45.455 0.00 0.00 36.34 2.12
3398 3591 2.372264 ACTGCCAGCATTGAATAGTGG 58.628 47.619 0.00 1.54 0.00 4.00
3400 3593 3.018856 CTGCCAGCATTGAATAGTGGAA 58.981 45.455 8.70 0.00 0.00 3.53
3401 3594 2.754552 TGCCAGCATTGAATAGTGGAAC 59.245 45.455 8.70 0.00 0.00 3.62
3415 3608 2.113860 TGGAACTGCCAGCATAGAAC 57.886 50.000 0.00 0.00 43.33 3.01
3416 3609 1.630369 TGGAACTGCCAGCATAGAACT 59.370 47.619 0.00 0.00 43.33 3.01
3417 3610 2.040278 TGGAACTGCCAGCATAGAACTT 59.960 45.455 0.00 0.00 43.33 2.66
3418 3611 3.263170 TGGAACTGCCAGCATAGAACTTA 59.737 43.478 0.00 0.00 43.33 2.24
3419 3612 3.623510 GGAACTGCCAGCATAGAACTTAC 59.376 47.826 0.00 0.00 36.34 2.34
3420 3613 4.508662 GAACTGCCAGCATAGAACTTACT 58.491 43.478 0.00 0.00 0.00 2.24
3504 3697 2.165437 AGCTGAGAAGTAGAGGAAAGCG 59.835 50.000 0.00 0.00 34.65 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.681264 AGTAACCACCAAAGCAGTTGC 59.319 47.619 0.00 0.00 42.49 4.17
2 3 5.705609 AATAGTAACCACCAAAGCAGTTG 57.294 39.130 0.00 0.00 36.94 3.16
3 4 5.010617 CCAAATAGTAACCACCAAAGCAGTT 59.989 40.000 0.00 0.00 0.00 3.16
4 5 4.522789 CCAAATAGTAACCACCAAAGCAGT 59.477 41.667 0.00 0.00 0.00 4.40
5 6 4.618227 GCCAAATAGTAACCACCAAAGCAG 60.618 45.833 0.00 0.00 0.00 4.24
6 7 3.257127 GCCAAATAGTAACCACCAAAGCA 59.743 43.478 0.00 0.00 0.00 3.91
7 8 3.257127 TGCCAAATAGTAACCACCAAAGC 59.743 43.478 0.00 0.00 0.00 3.51
8 9 4.279671 TGTGCCAAATAGTAACCACCAAAG 59.720 41.667 0.00 0.00 0.00 2.77
9 10 4.215908 TGTGCCAAATAGTAACCACCAAA 58.784 39.130 0.00 0.00 0.00 3.28
10 11 3.833732 TGTGCCAAATAGTAACCACCAA 58.166 40.909 0.00 0.00 0.00 3.67
11 12 3.510531 TGTGCCAAATAGTAACCACCA 57.489 42.857 0.00 0.00 0.00 4.17
12 13 5.167845 CAAATGTGCCAAATAGTAACCACC 58.832 41.667 0.00 0.00 0.00 4.61
13 14 5.167845 CCAAATGTGCCAAATAGTAACCAC 58.832 41.667 0.00 0.00 0.00 4.16
14 15 4.221703 CCCAAATGTGCCAAATAGTAACCA 59.778 41.667 0.00 0.00 0.00 3.67
15 16 4.464597 TCCCAAATGTGCCAAATAGTAACC 59.535 41.667 0.00 0.00 0.00 2.85
16 17 5.394115 CCTCCCAAATGTGCCAAATAGTAAC 60.394 44.000 0.00 0.00 0.00 2.50
17 18 4.709397 CCTCCCAAATGTGCCAAATAGTAA 59.291 41.667 0.00 0.00 0.00 2.24
18 19 4.277476 CCTCCCAAATGTGCCAAATAGTA 58.723 43.478 0.00 0.00 0.00 1.82
19 20 3.099141 CCTCCCAAATGTGCCAAATAGT 58.901 45.455 0.00 0.00 0.00 2.12
20 21 2.159057 GCCTCCCAAATGTGCCAAATAG 60.159 50.000 0.00 0.00 0.00 1.73
21 22 1.830477 GCCTCCCAAATGTGCCAAATA 59.170 47.619 0.00 0.00 0.00 1.40
22 23 0.614812 GCCTCCCAAATGTGCCAAAT 59.385 50.000 0.00 0.00 0.00 2.32
23 24 1.814772 CGCCTCCCAAATGTGCCAAA 61.815 55.000 0.00 0.00 0.00 3.28
24 25 2.274645 CGCCTCCCAAATGTGCCAA 61.275 57.895 0.00 0.00 0.00 4.52
25 26 2.676121 CGCCTCCCAAATGTGCCA 60.676 61.111 0.00 0.00 0.00 4.92
26 27 2.361104 TCGCCTCCCAAATGTGCC 60.361 61.111 0.00 0.00 0.00 5.01
27 28 2.409870 CCTCGCCTCCCAAATGTGC 61.410 63.158 0.00 0.00 0.00 4.57
28 29 0.322456 TTCCTCGCCTCCCAAATGTG 60.322 55.000 0.00 0.00 0.00 3.21
29 30 0.625849 ATTCCTCGCCTCCCAAATGT 59.374 50.000 0.00 0.00 0.00 2.71
30 31 1.027357 CATTCCTCGCCTCCCAAATG 58.973 55.000 0.00 0.00 0.00 2.32
31 32 0.918983 TCATTCCTCGCCTCCCAAAT 59.081 50.000 0.00 0.00 0.00 2.32
32 33 0.918983 ATCATTCCTCGCCTCCCAAA 59.081 50.000 0.00 0.00 0.00 3.28
33 34 0.181114 CATCATTCCTCGCCTCCCAA 59.819 55.000 0.00 0.00 0.00 4.12
34 35 0.982852 ACATCATTCCTCGCCTCCCA 60.983 55.000 0.00 0.00 0.00 4.37
35 36 0.250081 GACATCATTCCTCGCCTCCC 60.250 60.000 0.00 0.00 0.00 4.30
36 37 0.465705 TGACATCATTCCTCGCCTCC 59.534 55.000 0.00 0.00 0.00 4.30
37 38 1.539929 CCTGACATCATTCCTCGCCTC 60.540 57.143 0.00 0.00 0.00 4.70
38 39 0.467384 CCTGACATCATTCCTCGCCT 59.533 55.000 0.00 0.00 0.00 5.52
39 40 0.465705 TCCTGACATCATTCCTCGCC 59.534 55.000 0.00 0.00 0.00 5.54
40 41 1.936547 GTTCCTGACATCATTCCTCGC 59.063 52.381 0.00 0.00 0.00 5.03
41 42 3.251479 TGTTCCTGACATCATTCCTCG 57.749 47.619 0.00 0.00 32.00 4.63
42 43 4.337555 CCATTGTTCCTGACATCATTCCTC 59.662 45.833 0.00 0.00 38.26 3.71
43 44 4.264083 ACCATTGTTCCTGACATCATTCCT 60.264 41.667 0.00 0.00 38.26 3.36
44 45 4.019174 ACCATTGTTCCTGACATCATTCC 58.981 43.478 0.00 0.00 38.26 3.01
45 46 4.676196 GCACCATTGTTCCTGACATCATTC 60.676 45.833 0.00 0.00 38.26 2.67
46 47 3.194116 GCACCATTGTTCCTGACATCATT 59.806 43.478 0.00 0.00 38.26 2.57
47 48 2.756760 GCACCATTGTTCCTGACATCAT 59.243 45.455 0.00 0.00 38.26 2.45
48 49 2.161855 GCACCATTGTTCCTGACATCA 58.838 47.619 0.00 0.00 38.26 3.07
49 50 1.131126 CGCACCATTGTTCCTGACATC 59.869 52.381 0.00 0.00 38.26 3.06
50 51 1.167851 CGCACCATTGTTCCTGACAT 58.832 50.000 0.00 0.00 38.26 3.06
51 52 0.888736 CCGCACCATTGTTCCTGACA 60.889 55.000 0.00 0.00 36.19 3.58
52 53 0.889186 ACCGCACCATTGTTCCTGAC 60.889 55.000 0.00 0.00 0.00 3.51
53 54 0.605319 GACCGCACCATTGTTCCTGA 60.605 55.000 0.00 0.00 0.00 3.86
54 55 1.586154 GGACCGCACCATTGTTCCTG 61.586 60.000 0.00 0.00 0.00 3.86
55 56 1.303317 GGACCGCACCATTGTTCCT 60.303 57.895 0.00 0.00 0.00 3.36
56 57 0.035820 TAGGACCGCACCATTGTTCC 60.036 55.000 0.00 0.00 0.00 3.62
57 58 1.084289 GTAGGACCGCACCATTGTTC 58.916 55.000 0.00 0.00 0.00 3.18
58 59 0.398696 TGTAGGACCGCACCATTGTT 59.601 50.000 0.00 0.00 0.00 2.83
59 60 0.618458 ATGTAGGACCGCACCATTGT 59.382 50.000 0.00 0.00 0.00 2.71
60 61 1.299541 GATGTAGGACCGCACCATTG 58.700 55.000 0.00 0.00 0.00 2.82
61 62 0.180406 GGATGTAGGACCGCACCATT 59.820 55.000 0.00 0.00 0.00 3.16
62 63 0.691078 AGGATGTAGGACCGCACCAT 60.691 55.000 0.00 2.42 0.00 3.55
63 64 1.305802 AGGATGTAGGACCGCACCA 60.306 57.895 0.00 0.00 0.00 4.17
64 65 1.327690 TGAGGATGTAGGACCGCACC 61.328 60.000 0.00 0.00 31.64 5.01
65 66 0.753262 ATGAGGATGTAGGACCGCAC 59.247 55.000 0.00 0.00 38.61 5.34
66 67 1.040646 GATGAGGATGTAGGACCGCA 58.959 55.000 0.00 0.00 39.90 5.69
67 68 0.039074 CGATGAGGATGTAGGACCGC 60.039 60.000 0.00 0.00 0.00 5.68
68 69 1.001268 CACGATGAGGATGTAGGACCG 60.001 57.143 0.00 0.00 0.00 4.79
69 70 2.032620 ACACGATGAGGATGTAGGACC 58.967 52.381 0.00 0.00 0.00 4.46
70 71 2.223829 CCACACGATGAGGATGTAGGAC 60.224 54.545 0.00 0.00 28.90 3.85
77 78 1.613317 TTCGGCCACACGATGAGGAT 61.613 55.000 2.24 0.00 43.11 3.24
96 97 8.177119 TCAACTCCACATAAGCAATACTTTTT 57.823 30.769 0.00 0.00 39.97 1.94
127 128 4.915704 TGACGGTTTTAAAAGCAGTTCTG 58.084 39.130 25.15 12.93 36.24 3.02
138 139 5.473846 TGCATATGAGGTTTGACGGTTTTAA 59.526 36.000 6.97 0.00 0.00 1.52
139 140 5.004448 TGCATATGAGGTTTGACGGTTTTA 58.996 37.500 6.97 0.00 0.00 1.52
148 149 3.067180 GGTGGACATGCATATGAGGTTTG 59.933 47.826 6.97 0.00 37.73 2.93
149 150 3.290710 GGTGGACATGCATATGAGGTTT 58.709 45.455 6.97 0.00 37.73 3.27
152 153 1.143481 TGGGTGGACATGCATATGAGG 59.857 52.381 6.97 0.00 37.73 3.86
155 156 2.101249 GGTTTGGGTGGACATGCATATG 59.899 50.000 0.00 0.00 40.24 1.78
159 160 1.532794 GGGTTTGGGTGGACATGCA 60.533 57.895 0.00 0.00 0.00 3.96
175 176 0.392998 CCCATCGAGACACCAAAGGG 60.393 60.000 0.00 0.00 41.29 3.95
179 180 0.323629 GGAACCCATCGAGACACCAA 59.676 55.000 0.00 0.00 0.00 3.67
180 181 1.884075 CGGAACCCATCGAGACACCA 61.884 60.000 0.00 0.00 0.00 4.17
203 204 6.037720 ACATTTACGAACATTGTGTCTGTTGA 59.962 34.615 0.00 0.00 36.98 3.18
211 212 8.313227 GCATTATCAACATTTACGAACATTGTG 58.687 33.333 0.00 0.00 0.00 3.33
213 214 8.313227 GTGCATTATCAACATTTACGAACATTG 58.687 33.333 0.00 0.00 0.00 2.82
214 215 7.487829 GGTGCATTATCAACATTTACGAACATT 59.512 33.333 0.00 0.00 0.00 2.71
216 217 6.072452 TGGTGCATTATCAACATTTACGAACA 60.072 34.615 0.00 0.00 0.00 3.18
233 234 3.514645 GCGAATTCTGAAATGGTGCATT 58.485 40.909 3.52 0.00 35.39 3.56
240 241 1.658596 TCCGTCGCGAATTCTGAAATG 59.341 47.619 12.06 0.00 0.00 2.32
241 242 2.004583 TCCGTCGCGAATTCTGAAAT 57.995 45.000 12.06 0.00 0.00 2.17
257 258 4.838152 CACGCCCACTCCCATCCG 62.838 72.222 0.00 0.00 0.00 4.18
258 259 4.489771 CCACGCCCACTCCCATCC 62.490 72.222 0.00 0.00 0.00 3.51
263 264 1.303317 AAATCACCACGCCCACTCC 60.303 57.895 0.00 0.00 0.00 3.85
265 266 0.179004 TTCAAATCACCACGCCCACT 60.179 50.000 0.00 0.00 0.00 4.00
291 292 1.007502 TGCCAACAAGCACAATCGC 60.008 52.632 0.00 0.00 38.00 4.58
309 311 1.086067 CCTCAATGCGCTCGTGACAT 61.086 55.000 9.73 0.00 0.00 3.06
312 314 1.153765 CTCCTCAATGCGCTCGTGA 60.154 57.895 9.73 8.51 0.00 4.35
315 317 0.179111 TAACCTCCTCAATGCGCTCG 60.179 55.000 9.73 0.00 0.00 5.03
325 327 3.386402 AGTTCTAGCATGCTAACCTCCTC 59.614 47.826 26.71 13.18 0.00 3.71
335 337 2.753296 CCTCAGCTAGTTCTAGCATGC 58.247 52.381 26.62 10.51 45.11 4.06
341 343 2.952978 GCTAGTGCCTCAGCTAGTTCTA 59.047 50.000 0.00 0.00 40.80 2.10
362 364 4.409588 CAACGGCGTGTCGAAGCG 62.410 66.667 15.70 5.63 0.00 4.68
363 365 4.719616 GCAACGGCGTGTCGAAGC 62.720 66.667 15.70 7.69 0.00 3.86
373 375 2.049063 ACGAGTGAGAGCAACGGC 60.049 61.111 0.00 0.00 41.61 5.68
374 376 1.444553 GGACGAGTGAGAGCAACGG 60.445 63.158 0.00 0.00 32.85 4.44
375 377 0.730834 CTGGACGAGTGAGAGCAACG 60.731 60.000 0.00 0.00 34.09 4.10
376 378 0.598562 TCTGGACGAGTGAGAGCAAC 59.401 55.000 0.00 0.00 0.00 4.17
377 379 1.270826 CTTCTGGACGAGTGAGAGCAA 59.729 52.381 0.00 0.00 0.00 3.91
378 380 0.884514 CTTCTGGACGAGTGAGAGCA 59.115 55.000 0.00 0.00 0.00 4.26
379 381 0.172352 CCTTCTGGACGAGTGAGAGC 59.828 60.000 0.00 0.00 34.57 4.09
380 382 1.540267 ACCTTCTGGACGAGTGAGAG 58.460 55.000 0.00 0.00 37.04 3.20
381 383 1.996798 AACCTTCTGGACGAGTGAGA 58.003 50.000 0.00 0.00 37.04 3.27
382 384 2.821991 AAACCTTCTGGACGAGTGAG 57.178 50.000 0.00 0.00 37.04 3.51
383 385 2.432874 TGAAAACCTTCTGGACGAGTGA 59.567 45.455 0.00 0.00 37.04 3.41
384 386 2.833794 TGAAAACCTTCTGGACGAGTG 58.166 47.619 0.00 0.00 37.04 3.51
385 387 3.771577 ATGAAAACCTTCTGGACGAGT 57.228 42.857 0.00 0.00 37.04 4.18
392 394 7.609532 AGAAGATGACCTTATGAAAACCTTCTG 59.390 37.037 0.00 0.00 36.34 3.02
416 418 4.499865 CCGAAAGACTGTCTGAAGTGAAGA 60.500 45.833 11.71 0.00 0.00 2.87
430 432 2.297597 CTCTCTGGACAACCGAAAGACT 59.702 50.000 0.00 0.00 39.42 3.24
458 460 7.256286 GTGACTACTACGGTCTATTGTTTGAT 58.744 38.462 0.00 0.00 35.04 2.57
465 467 3.631227 GCTGGTGACTACTACGGTCTATT 59.369 47.826 0.00 0.00 35.04 1.73
467 469 2.026915 TGCTGGTGACTACTACGGTCTA 60.027 50.000 0.00 0.00 35.04 2.59
486 492 1.438814 CCCGCCAAAATCCTGATGC 59.561 57.895 0.00 0.00 0.00 3.91
492 498 0.035534 AAATTGCCCCGCCAAAATCC 60.036 50.000 0.00 0.00 0.00 3.01
500 506 1.873270 AAGACGGAAAATTGCCCCGC 61.873 55.000 11.76 6.56 46.54 6.13
502 508 0.966179 ACAAGACGGAAAATTGCCCC 59.034 50.000 0.00 0.00 0.00 5.80
547 553 2.727123 ATATGAACCGCCCACATTCA 57.273 45.000 0.00 0.00 36.81 2.57
598 604 2.552315 ACCGGAGTTACATTGCACAAAG 59.448 45.455 9.46 0.00 0.00 2.77
603 609 1.268352 GCAAACCGGAGTTACATTGCA 59.732 47.619 9.46 0.00 36.46 4.08
619 625 8.465999 TGTTAAAGAGAGTTTTTCAGATGCAAA 58.534 29.630 0.00 0.00 0.00 3.68
813 821 1.606601 TGGGGACTGAGGTGTCGAG 60.607 63.158 0.00 0.00 37.81 4.04
844 872 3.454371 GTAGGATGCGATGTACAACCT 57.546 47.619 0.00 5.16 42.38 3.50
888 985 1.480545 CAAGGGGCGGGATTTTAAAGG 59.519 52.381 0.00 0.00 0.00 3.11
984 1081 1.731433 CCATTCTTGGGCGGCTGATG 61.731 60.000 9.56 6.30 39.56 3.07
1608 1708 0.321564 TGGTGTTGAAGATGGAGCCG 60.322 55.000 0.00 0.00 0.00 5.52
2103 2203 0.832135 AGAAGCCAGAGTCGGGAACA 60.832 55.000 14.12 0.00 0.00 3.18
2229 2329 3.959991 GAGCTTCACGGCCAGGTCC 62.960 68.421 2.24 0.00 32.37 4.46
2484 2584 2.352915 GAGTCGCTGCCGATCTCG 60.353 66.667 0.00 0.00 46.38 4.04
2625 2725 0.812549 GTCACTCCTCCTCCTCGAAC 59.187 60.000 0.00 0.00 0.00 3.95
2631 2731 2.037527 ACCGGTCACTCCTCCTCC 59.962 66.667 0.00 0.00 0.00 4.30
2689 2804 7.816640 AGAAAATTCGCAAGCAGAATAACTAA 58.183 30.769 10.74 0.00 37.34 2.24
2690 2805 7.377766 AGAAAATTCGCAAGCAGAATAACTA 57.622 32.000 10.74 0.00 37.34 2.24
2691 2806 6.259550 AGAAAATTCGCAAGCAGAATAACT 57.740 33.333 10.74 8.58 37.34 2.24
2692 2807 6.934561 AAGAAAATTCGCAAGCAGAATAAC 57.065 33.333 10.74 7.16 37.34 1.89
2753 2873 1.926511 GCATGCCCAGGTTTCAGTCG 61.927 60.000 6.36 0.00 0.00 4.18
2756 2876 0.245539 CAAGCATGCCCAGGTTTCAG 59.754 55.000 15.66 0.00 0.00 3.02
2768 2888 3.000523 GGCATACAAAATTCGCAAGCATG 59.999 43.478 0.00 0.00 37.18 4.06
2770 2890 2.230992 AGGCATACAAAATTCGCAAGCA 59.769 40.909 0.00 0.00 37.18 3.91
2806 2926 3.152341 GCACCAGGGATAGAATTCATGG 58.848 50.000 8.44 8.00 32.85 3.66
2827 2947 4.232221 CCATTGCAGCAACTTAACTTCTG 58.768 43.478 10.85 1.07 0.00 3.02
2855 2975 3.688185 GGGTTGGAGAGGTTTAATCGAAC 59.312 47.826 0.00 0.00 32.76 3.95
2872 2992 2.037208 ATGCTTTCCCGGGGGTTG 59.963 61.111 23.50 9.97 36.47 3.77
2890 3010 4.767255 CGTCAGGCCTGCCCAGTC 62.767 72.222 28.91 11.89 36.58 3.51
2894 3014 3.036429 ATCTTCGTCAGGCCTGCCC 62.036 63.158 28.91 18.95 36.58 5.36
2895 3015 1.817099 CATCTTCGTCAGGCCTGCC 60.817 63.158 28.91 17.17 0.00 4.85
2897 3017 1.817099 GCCATCTTCGTCAGGCCTG 60.817 63.158 27.87 27.87 41.25 4.85
2901 3021 1.089920 CTTTGGCCATCTTCGTCAGG 58.910 55.000 6.09 0.00 0.00 3.86
2902 3022 1.813513 ACTTTGGCCATCTTCGTCAG 58.186 50.000 6.09 0.00 0.00 3.51
2903 3023 2.270352 AACTTTGGCCATCTTCGTCA 57.730 45.000 6.09 0.00 0.00 4.35
2904 3024 2.922335 GCAAACTTTGGCCATCTTCGTC 60.922 50.000 6.09 0.00 0.00 4.20
2905 3025 1.000274 GCAAACTTTGGCCATCTTCGT 60.000 47.619 6.09 0.00 0.00 3.85
2928 3054 3.576078 TTCACAAGGTGGATTCAGTGT 57.424 42.857 0.00 0.00 33.87 3.55
2941 3094 4.736464 GCCTTTAACTGGGTGTTTCACAAG 60.736 45.833 2.41 2.18 39.89 3.16
2976 3129 2.412525 CACGTGCTTGCTTGGCAA 59.587 55.556 0.82 0.00 46.80 4.52
2977 3130 3.594775 CCACGTGCTTGCTTGGCA 61.595 61.111 10.91 0.00 36.47 4.92
2978 3131 2.844451 TTCCACGTGCTTGCTTGGC 61.844 57.895 10.91 0.00 0.00 4.52
3029 3182 8.731326 GTTTAGAAAAGTTTAGTTGTCGCTTTC 58.269 33.333 0.00 0.00 0.00 2.62
3032 3185 7.549615 AGTTTAGAAAAGTTTAGTTGTCGCT 57.450 32.000 0.00 0.00 0.00 4.93
3062 3215 9.250624 GTTTAGATGAGTCGTAGCTGAATATTT 57.749 33.333 0.00 0.00 0.00 1.40
3121 3302 1.950909 TGGGTTTTAGCACCGACTTTG 59.049 47.619 0.00 0.00 37.76 2.77
3127 3308 1.804748 GACTCTTGGGTTTTAGCACCG 59.195 52.381 0.00 0.00 37.76 4.94
3145 3326 6.771749 AGATTCATCCATCCTGAATTCTTGAC 59.228 38.462 7.05 0.00 42.03 3.18
3155 3336 8.229253 TGAACAAAATAGATTCATCCATCCTG 57.771 34.615 0.00 0.00 0.00 3.86
3173 3354 9.066892 AGCATATAGAAAACTTGACTGAACAAA 57.933 29.630 0.00 0.00 0.00 2.83
3237 3418 3.240134 TTCAGAGCACGGCCAGTCC 62.240 63.158 2.24 0.00 0.00 3.85
3273 3462 0.947244 GGAAGCACAGACACACTTGG 59.053 55.000 0.00 0.00 0.00 3.61
3299 3488 9.703892 ACTTCTAATATTGCTATGAGCTTACAG 57.296 33.333 0.00 0.00 42.97 2.74
3351 3543 5.587443 CACTATTCATGTGCTGATTCTTCCA 59.413 40.000 0.00 0.00 32.72 3.53
3379 3572 2.646930 TCCACTATTCAATGCTGGCAG 58.353 47.619 10.94 10.94 0.00 4.85
3389 3582 1.350684 TGCTGGCAGTTCCACTATTCA 59.649 47.619 17.16 0.00 40.72 2.57
3390 3583 2.113860 TGCTGGCAGTTCCACTATTC 57.886 50.000 17.16 0.00 40.72 1.75
3393 3586 2.466846 TCTATGCTGGCAGTTCCACTA 58.533 47.619 17.16 0.00 40.72 2.74
3394 3587 1.279496 TCTATGCTGGCAGTTCCACT 58.721 50.000 17.16 0.00 40.72 4.00
3395 3588 1.740025 GTTCTATGCTGGCAGTTCCAC 59.260 52.381 17.16 0.00 40.72 4.02
3396 3589 1.630369 AGTTCTATGCTGGCAGTTCCA 59.370 47.619 17.16 6.04 44.18 3.53
3398 3591 4.508662 AGTAAGTTCTATGCTGGCAGTTC 58.491 43.478 17.16 0.20 0.00 3.01
3400 3593 3.515502 TGAGTAAGTTCTATGCTGGCAGT 59.484 43.478 17.16 0.00 0.00 4.40
3401 3594 3.868077 GTGAGTAAGTTCTATGCTGGCAG 59.132 47.826 10.94 10.94 0.00 4.85
3402 3595 3.260632 TGTGAGTAAGTTCTATGCTGGCA 59.739 43.478 0.00 0.00 0.00 4.92
3403 3596 3.861840 TGTGAGTAAGTTCTATGCTGGC 58.138 45.455 0.00 0.00 0.00 4.85
3404 3597 8.668510 AATTATGTGAGTAAGTTCTATGCTGG 57.331 34.615 0.00 0.00 0.00 4.85
3405 3598 8.483218 CGAATTATGTGAGTAAGTTCTATGCTG 58.517 37.037 0.00 0.00 0.00 4.41
3406 3599 8.198109 ACGAATTATGTGAGTAAGTTCTATGCT 58.802 33.333 0.00 0.00 0.00 3.79
3407 3600 8.354011 ACGAATTATGTGAGTAAGTTCTATGC 57.646 34.615 0.00 0.00 0.00 3.14
3408 3601 8.682895 CGACGAATTATGTGAGTAAGTTCTATG 58.317 37.037 0.00 0.00 0.00 2.23
3409 3602 8.618677 TCGACGAATTATGTGAGTAAGTTCTAT 58.381 33.333 0.00 0.00 0.00 1.98
3410 3603 7.907045 GTCGACGAATTATGTGAGTAAGTTCTA 59.093 37.037 0.00 0.00 0.00 2.10
3411 3604 6.746364 GTCGACGAATTATGTGAGTAAGTTCT 59.254 38.462 0.00 0.00 0.00 3.01
3412 3605 6.020837 GGTCGACGAATTATGTGAGTAAGTTC 60.021 42.308 9.92 0.00 0.00 3.01
3413 3606 5.803967 GGTCGACGAATTATGTGAGTAAGTT 59.196 40.000 9.92 0.00 0.00 2.66
3414 3607 5.106038 TGGTCGACGAATTATGTGAGTAAGT 60.106 40.000 9.92 0.00 0.00 2.24
3415 3608 5.337554 TGGTCGACGAATTATGTGAGTAAG 58.662 41.667 9.92 0.00 0.00 2.34
3416 3609 5.313520 TGGTCGACGAATTATGTGAGTAA 57.686 39.130 9.92 0.00 0.00 2.24
3417 3610 4.968812 TGGTCGACGAATTATGTGAGTA 57.031 40.909 9.92 0.00 0.00 2.59
3418 3611 3.861276 TGGTCGACGAATTATGTGAGT 57.139 42.857 9.92 0.00 0.00 3.41
3419 3612 4.566759 ACATTGGTCGACGAATTATGTGAG 59.433 41.667 21.39 11.81 0.00 3.51
3420 3613 4.328712 CACATTGGTCGACGAATTATGTGA 59.671 41.667 27.53 3.76 42.26 3.58
3504 3697 4.443266 ACCGCGCTGGAGCTTCTC 62.443 66.667 22.10 0.00 42.00 2.87


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

AutoCloner maintained by Alex Coulton.