Multiple sequence alignment - TraesCS7A01G402300

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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 TraesCS7A01G402300 chr7A 100.000 4619 0 0 1 4619 581428775 581433393 0.000000e+00 8530.0
1 TraesCS7A01G402300 chr7A 92.063 63 5 0 2585 2647 581431321 581431383 6.370000e-14 89.8
2 TraesCS7A01G402300 chr7A 92.063 63 5 0 2547 2609 581431359 581431421 6.370000e-14 89.8
3 TraesCS7A01G402300 chr7A 98.039 51 0 1 4466 4515 5870042 5870092 2.290000e-13 87.9
4 TraesCS7A01G402300 chr7A 98.039 51 0 1 4466 4515 18258124 18258074 2.290000e-13 87.9
5 TraesCS7A01G402300 chr7D 94.966 2900 80 23 1345 4205 510705022 510707894 0.000000e+00 4486.0
6 TraesCS7A01G402300 chr7D 87.679 560 35 16 778 1312 510704236 510704786 5.080000e-174 621.0
7 TraesCS7A01G402300 chr7D 85.942 377 15 12 4246 4619 510707983 510708324 7.300000e-98 368.0
8 TraesCS7A01G402300 chr7D 93.989 183 11 0 601 783 510702892 510703074 1.270000e-70 278.0
9 TraesCS7A01G402300 chr7D 88.235 85 10 0 462 546 570645310 570645226 8.180000e-18 102.0
10 TraesCS7A01G402300 chr7B 90.793 1879 66 40 561 2383 539229284 539231111 0.000000e+00 2412.0
11 TraesCS7A01G402300 chr7B 94.841 1318 51 10 2698 4004 539231544 539232855 0.000000e+00 2041.0
12 TraesCS7A01G402300 chr7B 88.315 368 16 7 4246 4613 539233104 539233444 2.570000e-112 416.0
13 TraesCS7A01G402300 chr7B 83.861 316 38 4 91 406 539227783 539228085 5.850000e-74 289.0
14 TraesCS7A01G402300 chr7B 93.750 128 4 3 4041 4164 539232857 539232984 6.100000e-44 189.0
15 TraesCS7A01G402300 chr7B 90.090 111 11 0 2499 2609 539231338 539231448 1.340000e-30 145.0
16 TraesCS7A01G402300 chr6B 76.329 790 160 19 2844 3621 229205662 229204888 9.310000e-107 398.0
17 TraesCS7A01G402300 chr6B 84.568 162 20 5 1688 1847 229206711 229206553 6.190000e-34 156.0
18 TraesCS7A01G402300 chr5D 90.741 270 16 3 3729 3991 390709879 390710146 7.350000e-93 351.0
19 TraesCS7A01G402300 chr5B 87.241 290 15 8 3730 4010 471137883 471138159 1.250000e-80 311.0
20 TraesCS7A01G402300 chr6D 75.355 422 64 27 1688 2097 131688609 131688216 2.860000e-37 167.0
21 TraesCS7A01G402300 chr6A 75.177 423 64 28 1688 2098 170013214 170012821 1.330000e-35 161.0
22 TraesCS7A01G402300 chr6A 84.756 164 20 5 1688 1849 169989973 169989813 4.780000e-35 159.0
23 TraesCS7A01G402300 chr6A 87.097 93 12 0 462 554 4415628 4415720 6.320000e-19 106.0
24 TraesCS7A01G402300 chr6A 97.959 49 1 0 4467 4515 39607552 39607504 8.230000e-13 86.1
25 TraesCS7A01G402300 chr6A 96.078 51 1 1 4466 4515 39566068 39566018 1.070000e-11 82.4
26 TraesCS7A01G402300 chr1B 86.957 92 12 0 462 553 2787047 2787138 2.270000e-18 104.0
27 TraesCS7A01G402300 chr2D 86.517 89 12 0 462 550 87812061 87811973 1.060000e-16 99.0
28 TraesCS7A01G402300 chr2D 87.209 86 9 2 462 546 538943507 538943423 3.800000e-16 97.1
29 TraesCS7A01G402300 chr2B 86.022 93 12 1 458 549 240186232 240186324 1.060000e-16 99.0
30 TraesCS7A01G402300 chr2B 85.106 94 12 2 462 554 212378021 212377929 1.370000e-15 95.3
31 TraesCS7A01G402300 chr1D 87.805 82 10 0 459 540 402722636 402722717 3.800000e-16 97.1
32 TraesCS7A01G402300 chr4B 85.106 94 12 2 462 554 540037684 540037776 1.370000e-15 95.3
33 TraesCS7A01G402300 chr4B 97.959 49 1 0 4467 4515 260433360 260433312 8.230000e-13 86.1
34 TraesCS7A01G402300 chr3B 98.039 51 0 1 4466 4515 814725426 814725376 2.290000e-13 87.9
35 TraesCS7A01G402300 chr2A 98.039 51 0 1 4466 4515 34854810 34854760 2.290000e-13 87.9


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 TraesCS7A01G402300 chr7A 581428775 581433393 4618 False 2903.200000 8530 94.708667 1 4619 3 chr7A.!!$F2 4618
1 TraesCS7A01G402300 chr7D 510702892 510708324 5432 False 1438.250000 4486 90.644000 601 4619 4 chr7D.!!$F1 4018
2 TraesCS7A01G402300 chr7B 539227783 539233444 5661 False 915.333333 2412 90.275000 91 4613 6 chr7B.!!$F1 4522
3 TraesCS7A01G402300 chr6B 229204888 229206711 1823 True 277.000000 398 80.448500 1688 3621 2 chr6B.!!$R1 1933

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
376 377 0.381445 TCAAACGGTTGTCGAGACGA 59.619 50.000 13.90 0.00 42.43 4.20 F
1249 3578 0.613777 GTGGATGGGACGGGGATATC 59.386 60.000 0.00 0.00 0.00 1.63 F
1308 3638 0.390735 GCGGTCTGTATTGAACGGGT 60.391 55.000 4.17 0.00 46.09 5.28 F
3132 6068 1.069022 CCCATGCTGTTGAACAACTCG 60.069 52.381 16.70 10.01 41.67 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 3618 0.390603 CCCGTTCAATACAGACCGCA 60.391 55.000 0.00 0.0 0.00 5.69 R
2504 5261 1.537202 GGACAACCACAGATGCTTCAC 59.463 52.381 2.07 0.0 35.97 3.18 R
3282 6218 0.249911 GCTTCGTGTTGACTCCACCT 60.250 55.000 0.00 0.0 0.00 4.00 R
4260 7269 0.679505 CACTCGTCTGGACAAAGGGA 59.320 55.000 1.63 0.0 0.00 4.20 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
36 37 5.493133 TTTTTACACAGGTGCTGTTGTAG 57.507 39.130 0.00 0.00 42.59 2.74
37 38 4.409718 TTTACACAGGTGCTGTTGTAGA 57.590 40.909 0.00 0.00 42.59 2.59
38 39 4.409718 TTACACAGGTGCTGTTGTAGAA 57.590 40.909 0.00 0.00 42.59 2.10
39 40 3.492102 ACACAGGTGCTGTTGTAGAAT 57.508 42.857 0.00 0.00 42.59 2.40
40 41 4.617253 ACACAGGTGCTGTTGTAGAATA 57.383 40.909 0.00 0.00 42.59 1.75
41 42 4.569943 ACACAGGTGCTGTTGTAGAATAG 58.430 43.478 0.00 0.00 42.59 1.73
42 43 3.935203 CACAGGTGCTGTTGTAGAATAGG 59.065 47.826 0.00 0.00 42.59 2.57
43 44 3.055094 ACAGGTGCTGTTGTAGAATAGGG 60.055 47.826 0.00 0.00 42.59 3.53
44 45 2.505819 AGGTGCTGTTGTAGAATAGGGG 59.494 50.000 0.00 0.00 0.00 4.79
45 46 2.289565 GTGCTGTTGTAGAATAGGGGC 58.710 52.381 0.00 0.00 0.00 5.80
46 47 1.134521 TGCTGTTGTAGAATAGGGGCG 60.135 52.381 0.00 0.00 0.00 6.13
47 48 1.810412 GCTGTTGTAGAATAGGGGCGG 60.810 57.143 0.00 0.00 0.00 6.13
48 49 1.760613 CTGTTGTAGAATAGGGGCGGA 59.239 52.381 0.00 0.00 0.00 5.54
49 50 1.760613 TGTTGTAGAATAGGGGCGGAG 59.239 52.381 0.00 0.00 0.00 4.63
50 51 1.070289 GTTGTAGAATAGGGGCGGAGG 59.930 57.143 0.00 0.00 0.00 4.30
51 52 0.471211 TGTAGAATAGGGGCGGAGGG 60.471 60.000 0.00 0.00 0.00 4.30
52 53 1.535687 TAGAATAGGGGCGGAGGGC 60.536 63.158 0.00 0.00 42.51 5.19
53 54 2.032356 TAGAATAGGGGCGGAGGGCT 62.032 60.000 0.00 0.00 42.94 5.19
54 55 2.368329 AATAGGGGCGGAGGGCTT 60.368 61.111 0.00 0.00 42.94 4.35
55 56 2.682582 GAATAGGGGCGGAGGGCTTG 62.683 65.000 0.00 0.00 42.94 4.01
56 57 4.733725 TAGGGGCGGAGGGCTTGT 62.734 66.667 0.00 0.00 42.94 3.16
73 74 3.980646 TTGTGCACATACAAGGTTCAC 57.019 42.857 22.39 0.00 35.75 3.18
74 75 2.924421 TGTGCACATACAAGGTTCACA 58.076 42.857 17.42 0.00 39.46 3.58
75 76 2.616376 TGTGCACATACAAGGTTCACAC 59.384 45.455 17.42 0.00 37.46 3.82
76 77 2.031157 GTGCACATACAAGGTTCACACC 60.031 50.000 13.17 0.00 44.67 4.16
88 89 4.336532 GGTTCACACCGACAAATACATC 57.663 45.455 0.00 0.00 31.60 3.06
89 90 3.126343 GGTTCACACCGACAAATACATCC 59.874 47.826 0.00 0.00 31.60 3.51
90 91 2.612604 TCACACCGACAAATACATCCG 58.387 47.619 0.00 0.00 0.00 4.18
91 92 1.663643 CACACCGACAAATACATCCGG 59.336 52.381 0.00 0.00 45.09 5.14
94 95 0.655733 CCGACAAATACATCCGGTGC 59.344 55.000 0.00 0.00 35.83 5.01
95 96 1.364721 CGACAAATACATCCGGTGCA 58.635 50.000 0.00 0.00 0.00 4.57
96 97 1.735018 CGACAAATACATCCGGTGCAA 59.265 47.619 0.00 0.00 0.00 4.08
97 98 2.354510 CGACAAATACATCCGGTGCAAT 59.645 45.455 0.00 0.00 0.00 3.56
98 99 3.694734 GACAAATACATCCGGTGCAATG 58.305 45.455 0.00 0.00 0.00 2.82
143 144 5.233225 TCTGAAACATTTGTGTTGTTGCAA 58.767 33.333 0.00 0.00 41.07 4.08
159 160 2.203625 AATGGTTTGCAGCGGGGT 60.204 55.556 0.00 0.00 0.00 4.95
160 161 1.836604 AATGGTTTGCAGCGGGGTT 60.837 52.632 0.00 0.00 0.00 4.11
161 162 2.098426 AATGGTTTGCAGCGGGGTTG 62.098 55.000 0.00 0.00 0.00 3.77
162 163 3.223589 GGTTTGCAGCGGGGTTGT 61.224 61.111 0.00 0.00 0.00 3.32
176 177 4.045783 CGGGGTTGTGTGTTTAAAACATC 58.954 43.478 0.00 0.00 44.35 3.06
177 178 4.202070 CGGGGTTGTGTGTTTAAAACATCT 60.202 41.667 0.00 0.00 44.35 2.90
183 184 6.546972 TGTGTGTTTAAAACATCTGCGATA 57.453 33.333 0.00 0.00 44.35 2.92
190 191 7.061673 TGTTTAAAACATCTGCGATATTGCAAC 59.938 33.333 18.27 9.94 39.54 4.17
191 192 4.700268 AAACATCTGCGATATTGCAACA 57.300 36.364 18.27 8.66 45.74 3.33
200 201 2.741517 CGATATTGCAACAGTGGTCACA 59.258 45.455 0.00 0.00 0.00 3.58
216 217 3.123621 GGTCACAGTGCGATTTCTGTAAG 59.876 47.826 0.00 0.00 42.05 2.34
237 238 9.238368 TGTAAGATAAGTATTGTTTCAAAGGGG 57.762 33.333 0.00 0.00 0.00 4.79
238 239 7.718334 AAGATAAGTATTGTTTCAAAGGGGG 57.282 36.000 0.00 0.00 0.00 5.40
265 266 4.699735 TGGTTCATACGAGATTGCAACAAT 59.300 37.500 0.00 0.00 0.00 2.71
266 267 5.030295 GGTTCATACGAGATTGCAACAATG 58.970 41.667 0.00 0.00 0.00 2.82
280 281 3.637998 AACAATGCTCTTGTTGCAGAG 57.362 42.857 14.52 0.00 44.04 3.35
281 282 1.884579 ACAATGCTCTTGTTGCAGAGG 59.115 47.619 3.19 0.00 44.04 3.69
335 336 2.952310 CGACACTCACATGGGAGAGATA 59.048 50.000 31.53 0.00 38.30 1.98
337 338 4.142160 CGACACTCACATGGGAGAGATAAA 60.142 45.833 31.53 0.00 38.30 1.40
339 340 6.319048 ACACTCACATGGGAGAGATAAAAT 57.681 37.500 31.53 3.04 38.30 1.82
341 342 6.070021 ACACTCACATGGGAGAGATAAAATGA 60.070 38.462 31.53 2.80 38.30 2.57
342 343 6.259608 CACTCACATGGGAGAGATAAAATGAC 59.740 42.308 31.53 0.00 38.30 3.06
344 345 6.962182 TCACATGGGAGAGATAAAATGACTT 58.038 36.000 0.00 0.00 0.00 3.01
359 360 5.598416 AATGACTTATCGTGACTCCATCA 57.402 39.130 0.00 0.00 33.79 3.07
368 369 2.218603 GTGACTCCATCAAACGGTTGT 58.781 47.619 13.90 0.00 39.72 3.32
375 376 1.124297 CATCAAACGGTTGTCGAGACG 59.876 52.381 13.90 0.00 42.43 4.18
376 377 0.381445 TCAAACGGTTGTCGAGACGA 59.619 50.000 13.90 0.00 42.43 4.20
384 385 2.541999 GGTTGTCGAGACGATGGATCTC 60.542 54.545 0.00 0.00 38.42 2.75
396 397 8.642935 AGACGATGGATCTCTTTAGATTATCA 57.357 34.615 0.00 0.00 42.73 2.15
397 398 9.253832 AGACGATGGATCTCTTTAGATTATCAT 57.746 33.333 0.00 0.00 42.73 2.45
406 407 8.195165 TCTCTTTAGATTATCATCCGACCAAT 57.805 34.615 0.00 0.00 0.00 3.16
407 408 9.309224 TCTCTTTAGATTATCATCCGACCAATA 57.691 33.333 0.00 0.00 0.00 1.90
409 410 8.027189 TCTTTAGATTATCATCCGACCAATACG 58.973 37.037 0.00 0.00 0.00 3.06
412 413 7.406031 AGATTATCATCCGACCAATACGTAT 57.594 36.000 1.14 1.14 0.00 3.06
418 419 3.018856 TCCGACCAATACGTATCACTGT 58.981 45.455 8.86 3.91 0.00 3.55
419 420 3.444742 TCCGACCAATACGTATCACTGTT 59.555 43.478 8.86 0.00 0.00 3.16
423 424 6.260377 CGACCAATACGTATCACTGTTCTAA 58.740 40.000 8.86 0.00 0.00 2.10
424 425 6.916387 CGACCAATACGTATCACTGTTCTAAT 59.084 38.462 8.86 0.00 0.00 1.73
426 427 9.740239 GACCAATACGTATCACTGTTCTAATAA 57.260 33.333 8.86 0.00 0.00 1.40
472 1597 9.884814 ACTGTCTTCTTATATTACTCCCTATGT 57.115 33.333 0.00 0.00 0.00 2.29
486 1611 9.877222 TTACTCCCTATGTCTCATAATGTAAGA 57.123 33.333 0.00 0.00 0.00 2.10
487 1612 8.964533 ACTCCCTATGTCTCATAATGTAAGAT 57.035 34.615 0.00 0.00 0.00 2.40
488 1613 8.811017 ACTCCCTATGTCTCATAATGTAAGATG 58.189 37.037 0.00 0.00 0.00 2.90
489 1614 8.727100 TCCCTATGTCTCATAATGTAAGATGT 57.273 34.615 0.00 0.00 0.00 3.06
490 1615 9.159254 TCCCTATGTCTCATAATGTAAGATGTT 57.841 33.333 0.00 0.00 0.00 2.71
491 1616 9.784531 CCCTATGTCTCATAATGTAAGATGTTT 57.215 33.333 0.00 0.00 0.00 2.83
511 1636 4.640789 TTTTTGACACTAATGCGGTGTT 57.359 36.364 0.00 0.00 46.23 3.32
512 1637 5.752892 TTTTTGACACTAATGCGGTGTTA 57.247 34.783 0.00 0.00 46.23 2.41
513 1638 5.752892 TTTTGACACTAATGCGGTGTTAA 57.247 34.783 0.00 0.00 46.23 2.01
514 1639 5.752892 TTTGACACTAATGCGGTGTTAAA 57.247 34.783 11.07 11.07 46.23 1.52
515 1640 5.752892 TTGACACTAATGCGGTGTTAAAA 57.247 34.783 0.00 0.00 46.23 1.52
516 1641 5.752892 TGACACTAATGCGGTGTTAAAAA 57.247 34.783 0.00 0.00 46.23 1.94
542 1667 8.287439 ACATCTTATATTATGAGACGGAGAGG 57.713 38.462 0.62 0.00 0.00 3.69
543 1668 7.340743 ACATCTTATATTATGAGACGGAGAGGG 59.659 40.741 0.62 0.00 0.00 4.30
544 1669 6.791371 TCTTATATTATGAGACGGAGAGGGT 58.209 40.000 0.00 0.00 0.00 4.34
545 1670 7.925622 TCTTATATTATGAGACGGAGAGGGTA 58.074 38.462 0.00 0.00 0.00 3.69
546 1671 8.047911 TCTTATATTATGAGACGGAGAGGGTAG 58.952 40.741 0.00 0.00 0.00 3.18
547 1672 3.947612 TTATGAGACGGAGAGGGTAGT 57.052 47.619 0.00 0.00 0.00 2.73
548 1673 2.830651 ATGAGACGGAGAGGGTAGTT 57.169 50.000 0.00 0.00 0.00 2.24
549 1674 2.599408 TGAGACGGAGAGGGTAGTTT 57.401 50.000 0.00 0.00 0.00 2.66
550 1675 3.726557 TGAGACGGAGAGGGTAGTTTA 57.273 47.619 0.00 0.00 0.00 2.01
551 1676 4.246712 TGAGACGGAGAGGGTAGTTTAT 57.753 45.455 0.00 0.00 0.00 1.40
552 1677 5.378230 TGAGACGGAGAGGGTAGTTTATA 57.622 43.478 0.00 0.00 0.00 0.98
553 1678 5.374921 TGAGACGGAGAGGGTAGTTTATAG 58.625 45.833 0.00 0.00 0.00 1.31
554 1679 5.131642 TGAGACGGAGAGGGTAGTTTATAGA 59.868 44.000 0.00 0.00 0.00 1.98
555 1680 5.623169 AGACGGAGAGGGTAGTTTATAGAG 58.377 45.833 0.00 0.00 0.00 2.43
556 1681 5.369110 AGACGGAGAGGGTAGTTTATAGAGA 59.631 44.000 0.00 0.00 0.00 3.10
557 1682 6.011122 ACGGAGAGGGTAGTTTATAGAGAA 57.989 41.667 0.00 0.00 0.00 2.87
558 1683 6.063404 ACGGAGAGGGTAGTTTATAGAGAAG 58.937 44.000 0.00 0.00 0.00 2.85
559 1684 6.063404 CGGAGAGGGTAGTTTATAGAGAAGT 58.937 44.000 0.00 0.00 0.00 3.01
641 1766 2.203983 TGGCTCCAGCTCCCTTGA 60.204 61.111 0.00 0.00 41.70 3.02
642 1767 2.270527 GGCTCCAGCTCCCTTGAC 59.729 66.667 0.00 0.00 41.70 3.18
696 1821 6.576662 TCCAATGGTTAGCAAATTTTACGA 57.423 33.333 0.00 0.00 0.00 3.43
718 1843 4.124851 TGCTCCGAGATAGGAAAGAAAC 57.875 45.455 0.00 0.00 40.25 2.78
774 1901 1.005215 AGAATCCTGCCCAAACTCCTG 59.995 52.381 0.00 0.00 0.00 3.86
1092 3412 4.821589 CAGCCTCGTTCTCGCCCC 62.822 72.222 0.00 0.00 36.96 5.80
1117 3437 1.269051 CCTGGTTTCTGGTTTCGTTGC 60.269 52.381 0.00 0.00 0.00 4.17
1121 3441 1.448922 TTTCTGGTTTCGTTGCCCCG 61.449 55.000 0.00 0.00 0.00 5.73
1122 3442 4.038080 CTGGTTTCGTTGCCCCGC 62.038 66.667 0.00 0.00 0.00 6.13
1123 3443 4.572571 TGGTTTCGTTGCCCCGCT 62.573 61.111 0.00 0.00 0.00 5.52
1124 3444 3.733960 GGTTTCGTTGCCCCGCTC 61.734 66.667 0.00 0.00 0.00 5.03
1125 3445 2.668550 GTTTCGTTGCCCCGCTCT 60.669 61.111 0.00 0.00 0.00 4.09
1126 3446 2.668212 TTTCGTTGCCCCGCTCTG 60.668 61.111 0.00 0.00 0.00 3.35
1127 3447 4.697756 TTCGTTGCCCCGCTCTGG 62.698 66.667 0.00 0.00 37.55 3.86
1135 3455 4.559063 CCCGCTCTGGCTGGATGG 62.559 72.222 0.00 0.00 44.11 3.51
1136 3456 4.559063 CCGCTCTGGCTGGATGGG 62.559 72.222 0.00 0.00 35.33 4.00
1137 3457 4.559063 CGCTCTGGCTGGATGGGG 62.559 72.222 0.00 0.00 36.09 4.96
1138 3458 4.891037 GCTCTGGCTGGATGGGGC 62.891 72.222 0.00 0.00 35.22 5.80
1180 3500 1.153086 CCTTTGCCGGATCTGGGAG 60.153 63.158 22.38 8.47 0.00 4.30
1186 3506 4.598894 CGGATCTGGGAGGCGCTG 62.599 72.222 7.64 0.00 0.00 5.18
1246 3574 2.772622 GGTGGATGGGACGGGGAT 60.773 66.667 0.00 0.00 0.00 3.85
1249 3578 0.613777 GTGGATGGGACGGGGATATC 59.386 60.000 0.00 0.00 0.00 1.63
1283 3612 1.373570 GCTTGTAGCGAGCCTGAAAT 58.626 50.000 0.00 0.00 35.00 2.17
1288 3618 3.674997 TGTAGCGAGCCTGAAATTTTCT 58.325 40.909 10.33 0.00 0.00 2.52
1304 3634 4.742438 TTTTCTGCGGTCTGTATTGAAC 57.258 40.909 0.00 0.00 0.00 3.18
1308 3638 0.390735 GCGGTCTGTATTGAACGGGT 60.391 55.000 4.17 0.00 46.09 5.28
1312 3642 3.404899 GGTCTGTATTGAACGGGTTTCA 58.595 45.455 0.00 0.00 42.83 2.69
1313 3643 4.007659 GGTCTGTATTGAACGGGTTTCAT 58.992 43.478 0.00 0.00 43.99 2.57
1314 3644 4.142687 GGTCTGTATTGAACGGGTTTCATG 60.143 45.833 0.00 0.00 43.99 3.07
1352 3872 2.799978 GTTCTTGCGGGGATTTGTTTTG 59.200 45.455 0.00 0.00 0.00 2.44
1354 3874 2.432510 TCTTGCGGGGATTTGTTTTGTT 59.567 40.909 0.00 0.00 0.00 2.83
1390 3922 5.499935 CAAAGATCTGAAGATGTGATTCGC 58.500 41.667 0.00 0.00 34.37 4.70
1440 3972 5.074377 TGGGGCAAATTATTAGCAGGATCTA 59.926 40.000 0.00 0.00 0.00 1.98
1522 4057 3.853330 CGCTGACGTTGGCATCCG 61.853 66.667 12.73 5.64 33.53 4.18
1549 4087 5.122396 GCCCAAAGCAGAAATATACGGATAG 59.878 44.000 0.00 0.00 42.97 2.08
2539 5296 6.216801 TGGTTGTCCACATAGTAGTGATAC 57.783 41.667 0.00 0.00 42.05 2.24
2710 5519 8.099537 CACCAGATGCCTCTCATTAGTTAATAT 58.900 37.037 0.00 0.00 35.05 1.28
2796 5606 8.547894 TGCATTATAAATCATCAGTCGTGTTAC 58.452 33.333 0.00 0.00 0.00 2.50
3057 5993 1.312815 AGTTCAACACAGCAGAAGGC 58.687 50.000 0.00 0.00 45.30 4.35
3132 6068 1.069022 CCCATGCTGTTGAACAACTCG 60.069 52.381 16.70 10.01 41.67 4.18
3178 6114 2.147387 AACGGTCACTTCCAGCCCT 61.147 57.895 0.00 0.00 0.00 5.19
3282 6218 1.110442 CTGGCGCCATTATTGGGAAA 58.890 50.000 32.87 1.17 43.84 3.13
3330 6266 0.255890 GAATGACTGGGGCCAAGCTA 59.744 55.000 8.19 0.00 0.00 3.32
3384 6320 2.859165 AAAACATTGAGCTCGAGGGA 57.141 45.000 19.36 0.00 0.00 4.20
3390 6326 0.456221 TTGAGCTCGAGGGATCGTTC 59.544 55.000 15.58 0.00 0.00 3.95
3408 6344 0.460109 TCGATCAGGTCAACCATGCG 60.460 55.000 1.33 0.29 38.89 4.73
3579 6521 0.108424 GAGACAGATGCCACTTCGCT 60.108 55.000 0.00 0.00 0.00 4.93
3626 6568 3.694058 CTGCGGCTTGAGGGATGCT 62.694 63.158 0.00 0.00 0.00 3.79
3630 6572 0.453390 CGGCTTGAGGGATGCTTTTC 59.547 55.000 0.00 0.00 0.00 2.29
3662 6604 8.623903 TCATGGCTTTTCATGATTAATAGTGAC 58.376 33.333 0.00 0.00 45.81 3.67
3694 6636 0.034670 AGCTCCAAATCTGAGGCCAC 60.035 55.000 5.01 0.00 0.00 5.01
3761 6703 2.171237 TGGGAGATACTGTCATGGCTTG 59.829 50.000 0.00 0.00 0.00 4.01
3763 6705 2.171448 GGAGATACTGTCATGGCTTGGT 59.829 50.000 0.00 0.00 0.00 3.67
3765 6707 4.265073 GAGATACTGTCATGGCTTGGTTT 58.735 43.478 0.00 0.00 0.00 3.27
4007 6956 6.248569 ACCGAACATCCTTGGTATTTAGAT 57.751 37.500 0.00 0.00 31.60 1.98
4008 6957 6.659824 ACCGAACATCCTTGGTATTTAGATT 58.340 36.000 0.00 0.00 31.60 2.40
4009 6958 7.798071 ACCGAACATCCTTGGTATTTAGATTA 58.202 34.615 0.00 0.00 31.60 1.75
4016 6965 9.739276 CATCCTTGGTATTTAGATTATAAGCCA 57.261 33.333 0.00 0.00 0.00 4.75
4196 7155 6.897259 TCAAAAGAATCGATAACCCTAACG 57.103 37.500 0.00 0.00 0.00 3.18
4210 7200 0.250553 CTAACGGTTTGCCTCACCCA 60.251 55.000 0.00 0.00 0.00 4.51
4215 7205 2.112029 GTTTGCCTCACCCAAACGT 58.888 52.632 1.84 0.00 41.55 3.99
4216 7206 0.248866 GTTTGCCTCACCCAAACGTG 60.249 55.000 0.00 0.00 41.55 4.49
4260 7269 4.250116 TGCTGAATGGCGTAAATTGTTT 57.750 36.364 0.00 0.00 34.52 2.83
4298 7307 2.098117 GTGATAATTGCCGCTTGCTCTT 59.902 45.455 0.00 0.00 42.00 2.85
4303 7312 2.010145 TTGCCGCTTGCTCTTAGTAG 57.990 50.000 0.00 0.00 42.00 2.57
4312 7321 7.371936 CCGCTTGCTCTTAGTAGAAGTATATT 58.628 38.462 0.00 0.00 0.00 1.28
4363 7372 3.149005 TGGAACACCCTTGGTATGTTC 57.851 47.619 18.27 18.27 37.67 3.18
4364 7373 2.443632 TGGAACACCCTTGGTATGTTCA 59.556 45.455 23.52 13.74 39.11 3.18
4365 7374 3.081804 GGAACACCCTTGGTATGTTCAG 58.918 50.000 23.52 0.48 39.11 3.02
4366 7375 2.879103 ACACCCTTGGTATGTTCAGG 57.121 50.000 0.00 0.00 32.11 3.86
4367 7376 1.354368 ACACCCTTGGTATGTTCAGGG 59.646 52.381 1.27 1.27 42.05 4.45
4368 7377 1.755200 ACCCTTGGTATGTTCAGGGT 58.245 50.000 2.68 2.68 44.23 4.34
4369 7378 2.574369 CACCCTTGGTATGTTCAGGGTA 59.426 50.000 8.44 0.00 46.97 3.69
4370 7379 3.202151 CACCCTTGGTATGTTCAGGGTAT 59.798 47.826 8.44 0.00 46.97 2.73
4371 7380 3.458487 ACCCTTGGTATGTTCAGGGTATC 59.542 47.826 6.97 0.00 46.83 2.24
4500 7509 6.587990 ACACTGATCAACATTTCTCTAACTCG 59.412 38.462 0.00 0.00 0.00 4.18
4508 7517 6.837471 ACATTTCTCTAACTCGGACTACTT 57.163 37.500 0.00 0.00 0.00 2.24
4509 7518 7.229581 ACATTTCTCTAACTCGGACTACTTT 57.770 36.000 0.00 0.00 0.00 2.66
4510 7519 8.345724 ACATTTCTCTAACTCGGACTACTTTA 57.654 34.615 0.00 0.00 0.00 1.85
4511 7520 8.242739 ACATTTCTCTAACTCGGACTACTTTAC 58.757 37.037 0.00 0.00 0.00 2.01
4512 7521 7.750229 TTTCTCTAACTCGGACTACTTTACA 57.250 36.000 0.00 0.00 0.00 2.41
4513 7522 6.734104 TCTCTAACTCGGACTACTTTACAC 57.266 41.667 0.00 0.00 0.00 2.90
4535 7544 6.317140 ACACTTACACAGCATCCAAATCATAG 59.683 38.462 0.00 0.00 0.00 2.23
4578 7590 6.710744 CCTACAAAAGTCCTCTCAAAAGCTAA 59.289 38.462 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.186942 TCTACAACAGCACCTGTGTAAAAA 58.813 37.500 0.00 0.00 44.62 1.94
15 16 4.771903 TCTACAACAGCACCTGTGTAAAA 58.228 39.130 0.00 0.00 44.62 1.52
16 17 4.409718 TCTACAACAGCACCTGTGTAAA 57.590 40.909 0.00 0.00 44.62 2.01
17 18 4.409718 TTCTACAACAGCACCTGTGTAA 57.590 40.909 0.00 0.00 44.62 2.41
18 19 4.617253 ATTCTACAACAGCACCTGTGTA 57.383 40.909 0.00 3.82 44.62 2.90
19 20 3.492102 ATTCTACAACAGCACCTGTGT 57.508 42.857 0.00 2.93 44.62 3.72
20 21 3.935203 CCTATTCTACAACAGCACCTGTG 59.065 47.826 0.00 0.00 44.62 3.66
22 23 3.535561 CCCTATTCTACAACAGCACCTG 58.464 50.000 0.00 0.00 37.52 4.00
23 24 2.505819 CCCCTATTCTACAACAGCACCT 59.494 50.000 0.00 0.00 0.00 4.00
24 25 2.919228 CCCCTATTCTACAACAGCACC 58.081 52.381 0.00 0.00 0.00 5.01
25 26 2.289565 GCCCCTATTCTACAACAGCAC 58.710 52.381 0.00 0.00 0.00 4.40
26 27 1.134521 CGCCCCTATTCTACAACAGCA 60.135 52.381 0.00 0.00 0.00 4.41
27 28 1.583054 CGCCCCTATTCTACAACAGC 58.417 55.000 0.00 0.00 0.00 4.40
28 29 1.760613 TCCGCCCCTATTCTACAACAG 59.239 52.381 0.00 0.00 0.00 3.16
29 30 1.760613 CTCCGCCCCTATTCTACAACA 59.239 52.381 0.00 0.00 0.00 3.33
30 31 1.070289 CCTCCGCCCCTATTCTACAAC 59.930 57.143 0.00 0.00 0.00 3.32
31 32 1.420430 CCTCCGCCCCTATTCTACAA 58.580 55.000 0.00 0.00 0.00 2.41
32 33 0.471211 CCCTCCGCCCCTATTCTACA 60.471 60.000 0.00 0.00 0.00 2.74
33 34 1.828461 GCCCTCCGCCCCTATTCTAC 61.828 65.000 0.00 0.00 0.00 2.59
34 35 1.535687 GCCCTCCGCCCCTATTCTA 60.536 63.158 0.00 0.00 0.00 2.10
35 36 2.849646 GCCCTCCGCCCCTATTCT 60.850 66.667 0.00 0.00 0.00 2.40
36 37 2.452937 AAGCCCTCCGCCCCTATTC 61.453 63.158 0.00 0.00 38.78 1.75
37 38 2.368329 AAGCCCTCCGCCCCTATT 60.368 61.111 0.00 0.00 38.78 1.73
38 39 3.171388 CAAGCCCTCCGCCCCTAT 61.171 66.667 0.00 0.00 38.78 2.57
39 40 4.733725 ACAAGCCCTCCGCCCCTA 62.734 66.667 0.00 0.00 38.78 3.53
45 46 1.078497 TATGTGCACAAGCCCTCCG 60.078 57.895 25.72 0.00 41.13 4.63
46 47 0.322456 TGTATGTGCACAAGCCCTCC 60.322 55.000 25.72 7.14 41.13 4.30
47 48 1.470098 CTTGTATGTGCACAAGCCCTC 59.530 52.381 25.72 10.85 46.37 4.30
48 49 1.538047 CTTGTATGTGCACAAGCCCT 58.462 50.000 25.72 9.59 46.37 5.19
51 52 6.276854 TGTGAACCTTGTATGTGCACAAGC 62.277 45.833 25.72 19.16 46.68 4.01
52 53 3.314913 TGTGAACCTTGTATGTGCACAAG 59.685 43.478 25.72 16.30 46.68 3.16
53 54 3.282885 TGTGAACCTTGTATGTGCACAA 58.717 40.909 25.72 10.60 46.68 3.33
55 56 2.031157 GGTGTGAACCTTGTATGTGCAC 60.031 50.000 10.75 10.75 41.77 4.57
56 57 2.226330 GGTGTGAACCTTGTATGTGCA 58.774 47.619 0.00 0.00 0.00 4.57
57 58 1.196808 CGGTGTGAACCTTGTATGTGC 59.803 52.381 0.00 0.00 0.00 4.57
58 59 2.478894 GTCGGTGTGAACCTTGTATGTG 59.521 50.000 0.00 0.00 0.00 3.21
59 60 2.103432 TGTCGGTGTGAACCTTGTATGT 59.897 45.455 0.00 0.00 0.00 2.29
60 61 2.761559 TGTCGGTGTGAACCTTGTATG 58.238 47.619 0.00 0.00 0.00 2.39
61 62 3.478857 TTGTCGGTGTGAACCTTGTAT 57.521 42.857 0.00 0.00 0.00 2.29
62 63 2.983907 TTGTCGGTGTGAACCTTGTA 57.016 45.000 0.00 0.00 0.00 2.41
63 64 2.116827 TTTGTCGGTGTGAACCTTGT 57.883 45.000 0.00 0.00 0.00 3.16
64 65 3.562141 TGTATTTGTCGGTGTGAACCTTG 59.438 43.478 0.00 0.00 0.00 3.61
65 66 3.811083 TGTATTTGTCGGTGTGAACCTT 58.189 40.909 0.00 0.00 0.00 3.50
66 67 3.478857 TGTATTTGTCGGTGTGAACCT 57.521 42.857 0.00 0.00 0.00 3.50
67 68 3.126343 GGATGTATTTGTCGGTGTGAACC 59.874 47.826 0.00 0.00 0.00 3.62
68 69 3.181524 CGGATGTATTTGTCGGTGTGAAC 60.182 47.826 0.00 0.00 0.00 3.18
69 70 2.997303 CGGATGTATTTGTCGGTGTGAA 59.003 45.455 0.00 0.00 0.00 3.18
70 71 2.612604 CGGATGTATTTGTCGGTGTGA 58.387 47.619 0.00 0.00 0.00 3.58
71 72 1.663643 CCGGATGTATTTGTCGGTGTG 59.336 52.381 0.00 0.00 36.38 3.82
72 73 2.018542 CCGGATGTATTTGTCGGTGT 57.981 50.000 0.00 0.00 36.38 4.16
75 76 0.655733 GCACCGGATGTATTTGTCGG 59.344 55.000 9.46 0.00 45.42 4.79
76 77 1.364721 TGCACCGGATGTATTTGTCG 58.635 50.000 9.46 0.00 0.00 4.35
77 78 3.694734 CATTGCACCGGATGTATTTGTC 58.305 45.455 9.46 0.00 0.00 3.18
78 79 2.159254 GCATTGCACCGGATGTATTTGT 60.159 45.455 9.46 0.00 0.00 2.83
79 80 2.099592 AGCATTGCACCGGATGTATTTG 59.900 45.455 9.46 5.05 0.00 2.32
80 81 2.378038 AGCATTGCACCGGATGTATTT 58.622 42.857 9.46 0.00 0.00 1.40
81 82 2.057137 AGCATTGCACCGGATGTATT 57.943 45.000 9.46 0.00 0.00 1.89
82 83 2.057137 AAGCATTGCACCGGATGTAT 57.943 45.000 9.46 0.00 0.00 2.29
83 84 1.472082 CAAAGCATTGCACCGGATGTA 59.528 47.619 9.46 0.00 0.00 2.29
84 85 0.244450 CAAAGCATTGCACCGGATGT 59.756 50.000 9.46 0.00 0.00 3.06
85 86 3.038946 CAAAGCATTGCACCGGATG 57.961 52.632 9.46 1.59 0.00 3.51
94 95 3.665745 AACCCTAGTTGCAAAGCATTG 57.334 42.857 0.00 0.00 38.76 2.82
95 96 4.772100 ACATAACCCTAGTTGCAAAGCATT 59.228 37.500 0.00 0.00 38.76 3.56
96 97 4.344104 ACATAACCCTAGTTGCAAAGCAT 58.656 39.130 0.00 0.00 38.76 3.79
97 98 3.761897 ACATAACCCTAGTTGCAAAGCA 58.238 40.909 0.00 0.00 36.68 3.91
98 99 4.783764 AACATAACCCTAGTTGCAAAGC 57.216 40.909 0.00 0.00 36.68 3.51
143 144 2.203625 AACCCCGCTGCAAACCAT 60.204 55.556 0.00 0.00 0.00 3.55
151 152 1.025812 TTAAACACACAACCCCGCTG 58.974 50.000 0.00 0.00 0.00 5.18
153 154 2.195096 GTTTTAAACACACAACCCCGC 58.805 47.619 2.62 0.00 0.00 6.13
155 156 5.047188 CAGATGTTTTAAACACACAACCCC 58.953 41.667 13.01 0.00 45.50 4.95
157 158 4.206200 CGCAGATGTTTTAAACACACAACC 59.794 41.667 13.01 0.00 45.50 3.77
159 160 5.236655 TCGCAGATGTTTTAAACACACAA 57.763 34.783 13.01 0.00 45.50 3.33
160 161 4.884458 TCGCAGATGTTTTAAACACACA 57.116 36.364 13.01 0.59 45.50 3.72
161 162 7.461416 GCAATATCGCAGATGTTTTAAACACAC 60.461 37.037 13.01 10.13 45.50 3.82
162 163 6.526325 GCAATATCGCAGATGTTTTAAACACA 59.474 34.615 13.01 0.00 45.50 3.72
176 177 1.739466 ACCACTGTTGCAATATCGCAG 59.261 47.619 0.59 7.46 44.14 5.18
177 178 1.737236 GACCACTGTTGCAATATCGCA 59.263 47.619 0.59 0.00 41.03 5.10
183 184 1.677576 CACTGTGACCACTGTTGCAAT 59.322 47.619 0.59 0.00 40.73 3.56
190 191 1.195448 GAAATCGCACTGTGACCACTG 59.805 52.381 12.86 5.64 36.50 3.66
191 192 1.070758 AGAAATCGCACTGTGACCACT 59.929 47.619 12.86 0.00 0.00 4.00
200 201 9.035607 CAATACTTATCTTACAGAAATCGCACT 57.964 33.333 0.00 0.00 0.00 4.40
236 237 3.771577 ATCTCGTATGAACCATTCCCC 57.228 47.619 0.00 0.00 0.00 4.81
237 238 3.251004 GCAATCTCGTATGAACCATTCCC 59.749 47.826 0.00 0.00 0.00 3.97
238 239 3.876914 TGCAATCTCGTATGAACCATTCC 59.123 43.478 0.00 0.00 0.00 3.01
239 240 5.163764 TGTTGCAATCTCGTATGAACCATTC 60.164 40.000 0.59 0.00 0.00 2.67
242 243 3.669536 TGTTGCAATCTCGTATGAACCA 58.330 40.909 0.59 0.00 0.00 3.67
265 266 1.673923 CGATCCTCTGCAACAAGAGCA 60.674 52.381 0.00 0.00 42.08 4.26
266 267 1.005340 CGATCCTCTGCAACAAGAGC 58.995 55.000 0.00 0.00 42.08 4.09
267 268 2.094286 ACTCGATCCTCTGCAACAAGAG 60.094 50.000 0.00 0.00 42.90 2.85
269 270 1.998315 CACTCGATCCTCTGCAACAAG 59.002 52.381 0.00 0.00 0.00 3.16
270 271 1.941209 GCACTCGATCCTCTGCAACAA 60.941 52.381 0.00 0.00 0.00 2.83
271 272 0.390340 GCACTCGATCCTCTGCAACA 60.390 55.000 0.00 0.00 0.00 3.33
272 273 0.390340 TGCACTCGATCCTCTGCAAC 60.390 55.000 3.89 0.00 36.71 4.17
273 274 0.321346 TTGCACTCGATCCTCTGCAA 59.679 50.000 12.32 12.32 45.13 4.08
274 275 0.390340 GTTGCACTCGATCCTCTGCA 60.390 55.000 2.50 2.50 37.86 4.41
275 276 0.390340 TGTTGCACTCGATCCTCTGC 60.390 55.000 0.00 0.00 0.00 4.26
276 277 1.067283 AGTGTTGCACTCGATCCTCTG 60.067 52.381 0.00 0.00 41.21 3.35
277 278 1.261480 AGTGTTGCACTCGATCCTCT 58.739 50.000 0.00 0.00 41.21 3.69
278 279 1.728971 CAAGTGTTGCACTCGATCCTC 59.271 52.381 2.04 0.00 44.62 3.71
279 280 1.609061 CCAAGTGTTGCACTCGATCCT 60.609 52.381 2.04 0.00 44.62 3.24
280 281 0.798776 CCAAGTGTTGCACTCGATCC 59.201 55.000 2.04 0.00 44.62 3.36
281 282 0.166814 GCCAAGTGTTGCACTCGATC 59.833 55.000 2.04 0.00 44.62 3.69
335 336 6.406370 TGATGGAGTCACGATAAGTCATTTT 58.594 36.000 0.00 0.00 0.00 1.82
337 338 5.598416 TGATGGAGTCACGATAAGTCATT 57.402 39.130 0.00 0.00 0.00 2.57
339 340 5.168569 GTTTGATGGAGTCACGATAAGTCA 58.831 41.667 0.00 0.00 36.32 3.41
341 342 4.174009 CGTTTGATGGAGTCACGATAAGT 58.826 43.478 0.00 0.00 36.32 2.24
342 343 3.551890 CCGTTTGATGGAGTCACGATAAG 59.448 47.826 0.00 0.00 36.32 1.73
344 345 2.494471 ACCGTTTGATGGAGTCACGATA 59.506 45.455 0.00 0.00 36.32 2.92
359 360 1.415374 CATCGTCTCGACAACCGTTT 58.585 50.000 0.00 0.00 39.18 3.60
368 369 4.704965 TCTAAAGAGATCCATCGTCTCGA 58.295 43.478 0.00 0.00 45.26 4.04
375 376 8.690884 TCGGATGATAATCTAAAGAGATCCATC 58.309 37.037 0.00 12.04 41.87 3.51
376 377 8.474025 GTCGGATGATAATCTAAAGAGATCCAT 58.526 37.037 0.00 0.00 41.87 3.41
384 385 7.813148 ACGTATTGGTCGGATGATAATCTAAAG 59.187 37.037 0.00 0.00 0.00 1.85
396 397 3.635373 ACAGTGATACGTATTGGTCGGAT 59.365 43.478 9.92 0.00 34.35 4.18
397 398 3.018856 ACAGTGATACGTATTGGTCGGA 58.981 45.455 9.92 0.00 0.00 4.55
429 430 9.969001 AGAAGACAGTTAAACTCTAGAGATAGT 57.031 33.333 26.57 13.15 0.00 2.12
463 1588 8.811017 ACATCTTACATTATGAGACATAGGGAG 58.189 37.037 0.00 0.00 0.00 4.30
465 1590 9.784531 AAACATCTTACATTATGAGACATAGGG 57.215 33.333 0.00 0.00 0.00 3.53
490 1615 7.544566 TTTTTAACACCGCATTAGTGTCAAAAA 59.455 29.630 11.78 11.78 45.97 1.94
516 1641 8.744652 CCTCTCCGTCTCATAATATAAGATGTT 58.255 37.037 0.00 0.00 0.00 2.71
517 1642 7.340743 CCCTCTCCGTCTCATAATATAAGATGT 59.659 40.741 0.00 0.00 0.00 3.06
518 1643 7.340743 ACCCTCTCCGTCTCATAATATAAGATG 59.659 40.741 0.00 0.00 0.00 2.90
519 1644 7.415086 ACCCTCTCCGTCTCATAATATAAGAT 58.585 38.462 0.00 0.00 0.00 2.40
520 1645 6.791371 ACCCTCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
521 1646 7.830201 ACTACCCTCTCCGTCTCATAATATAAG 59.170 40.741 0.00 0.00 0.00 1.73
522 1647 7.696981 ACTACCCTCTCCGTCTCATAATATAA 58.303 38.462 0.00 0.00 0.00 0.98
523 1648 7.268212 ACTACCCTCTCCGTCTCATAATATA 57.732 40.000 0.00 0.00 0.00 0.86
524 1649 6.142259 ACTACCCTCTCCGTCTCATAATAT 57.858 41.667 0.00 0.00 0.00 1.28
525 1650 5.579753 ACTACCCTCTCCGTCTCATAATA 57.420 43.478 0.00 0.00 0.00 0.98
526 1651 4.456662 ACTACCCTCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
527 1652 3.947612 ACTACCCTCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
528 1653 3.947612 AACTACCCTCTCCGTCTCATA 57.052 47.619 0.00 0.00 0.00 2.15
529 1654 2.830651 AACTACCCTCTCCGTCTCAT 57.169 50.000 0.00 0.00 0.00 2.90
530 1655 2.599408 AAACTACCCTCTCCGTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
531 1656 5.619220 TCTATAAACTACCCTCTCCGTCTC 58.381 45.833 0.00 0.00 0.00 3.36
532 1657 5.369110 TCTCTATAAACTACCCTCTCCGTCT 59.631 44.000 0.00 0.00 0.00 4.18
533 1658 5.619220 TCTCTATAAACTACCCTCTCCGTC 58.381 45.833 0.00 0.00 0.00 4.79
534 1659 5.643421 TCTCTATAAACTACCCTCTCCGT 57.357 43.478 0.00 0.00 0.00 4.69
535 1660 6.063404 ACTTCTCTATAAACTACCCTCTCCG 58.937 44.000 0.00 0.00 0.00 4.63
536 1661 8.219868 ACTACTTCTCTATAAACTACCCTCTCC 58.780 40.741 0.00 0.00 0.00 3.71
579 1704 6.935208 GCCTCCCGTATAACTTCAATCTTAAT 59.065 38.462 0.00 0.00 0.00 1.40
588 1713 3.893813 TCCTTAGCCTCCCGTATAACTTC 59.106 47.826 0.00 0.00 0.00 3.01
638 1763 2.661537 CAGGTGCGCTCGTGTCAA 60.662 61.111 20.59 0.00 0.00 3.18
696 1821 4.698575 GTTTCTTTCCTATCTCGGAGCAT 58.301 43.478 0.00 0.00 33.89 3.79
718 1843 1.532868 CTGGAGCCAGTTTTTGTCTCG 59.467 52.381 8.38 0.00 39.10 4.04
744 1871 0.463474 GCAGGATTCTGGCTGGAGAC 60.463 60.000 2.40 0.00 41.19 3.36
774 1901 1.052617 GCTCTGGTAAGGAGGGATCC 58.947 60.000 1.92 1.92 0.00 3.36
917 3228 2.962421 CCTAGGCTAGGGTTTCTCTCTG 59.038 54.545 29.55 2.43 42.42 3.35
1091 3411 1.435346 AACCAGAAACCAGGAGGGGG 61.435 60.000 0.00 0.00 42.91 5.40
1092 3412 0.482887 AAACCAGAAACCAGGAGGGG 59.517 55.000 0.00 0.00 42.91 4.79
1093 3413 1.882352 CGAAACCAGAAACCAGGAGGG 60.882 57.143 0.00 0.00 44.81 4.30
1094 3414 1.202770 ACGAAACCAGAAACCAGGAGG 60.203 52.381 0.00 0.00 42.21 4.30
1121 3441 4.891037 GCCCCATCCAGCCAGAGC 62.891 72.222 0.00 0.00 40.32 4.09
1122 3442 3.095163 AGCCCCATCCAGCCAGAG 61.095 66.667 0.00 0.00 0.00 3.35
1123 3443 3.092511 GAGCCCCATCCAGCCAGA 61.093 66.667 0.00 0.00 0.00 3.86
1124 3444 4.201122 GGAGCCCCATCCAGCCAG 62.201 72.222 0.00 0.00 39.34 4.85
1125 3445 2.856208 TAAGGAGCCCCATCCAGCCA 62.856 60.000 0.00 0.00 42.26 4.75
1126 3446 2.061790 CTAAGGAGCCCCATCCAGCC 62.062 65.000 0.00 0.00 42.26 4.85
1127 3447 1.453669 CTAAGGAGCCCCATCCAGC 59.546 63.158 0.00 0.00 42.26 4.85
1128 3448 1.422161 CCCTAAGGAGCCCCATCCAG 61.422 65.000 0.00 0.00 42.26 3.86
1129 3449 1.385915 CCCTAAGGAGCCCCATCCA 60.386 63.158 0.00 0.00 42.26 3.41
1132 3452 1.288037 GAAAACCCTAAGGAGCCCCAT 59.712 52.381 0.00 0.00 36.73 4.00
1133 3453 0.702316 GAAAACCCTAAGGAGCCCCA 59.298 55.000 0.00 0.00 36.73 4.96
1135 3455 0.327259 ACGAAAACCCTAAGGAGCCC 59.673 55.000 0.00 0.00 36.73 5.19
1136 3456 2.082231 GAACGAAAACCCTAAGGAGCC 58.918 52.381 0.00 0.00 36.73 4.70
1137 3457 2.082231 GGAACGAAAACCCTAAGGAGC 58.918 52.381 0.00 0.00 36.73 4.70
1138 3458 2.708051 GGGAACGAAAACCCTAAGGAG 58.292 52.381 0.00 0.00 42.56 3.69
1224 3552 2.435938 CGTCCCATCCACCAACCG 60.436 66.667 0.00 0.00 0.00 4.44
1246 3574 1.228894 CTCCTAGCAGCCCCCGATA 60.229 63.158 0.00 0.00 0.00 2.92
1283 3612 3.185594 CGTTCAATACAGACCGCAGAAAA 59.814 43.478 0.00 0.00 0.00 2.29
1288 3618 0.390603 CCCGTTCAATACAGACCGCA 60.391 55.000 0.00 0.00 0.00 5.69
1304 3634 1.213537 CAGCAAGCCATGAAACCCG 59.786 57.895 0.00 0.00 0.00 5.28
1327 3657 1.743394 CAAATCCCCGCAAGAACCTAC 59.257 52.381 0.00 0.00 43.02 3.18
1377 3909 4.510038 AAAAGCAAGCGAATCACATCTT 57.490 36.364 0.00 0.00 0.00 2.40
1440 3972 6.240060 CCTCTCTACCAGAATAGTACTAGCCT 60.240 46.154 8.85 5.02 0.00 4.58
1549 4087 6.856426 GCTATGCCAACGATTTAAATTAGGAC 59.144 38.462 1.43 1.11 0.00 3.85
2329 4926 6.595682 ACCTGATTACCTCCACATAATGAAG 58.404 40.000 0.00 0.00 0.00 3.02
2340 4937 5.308237 ACTTCCATGATACCTGATTACCTCC 59.692 44.000 0.00 0.00 0.00 4.30
2504 5261 1.537202 GGACAACCACAGATGCTTCAC 59.463 52.381 2.07 0.00 35.97 3.18
2558 5315 8.377034 AGTGTACAGACGATACTTAGATCCTAT 58.623 37.037 0.00 0.00 0.00 2.57
2571 5328 4.941873 TCTGATGTGTAGTGTACAGACGAT 59.058 41.667 0.00 0.00 39.77 3.73
2609 5366 5.638596 TTGATGTGTAGTGTACAGACGAT 57.361 39.130 0.00 0.00 39.77 3.73
2757 5566 8.517056 TGATTTATAATGCAGCCAATACTGATG 58.483 33.333 0.00 0.00 40.25 3.07
2796 5606 6.573725 GCGAACTTACACAACAATCTAAACTG 59.426 38.462 0.00 0.00 0.00 3.16
3057 5993 3.496331 ACACTTGTTCCCCCATTTACAG 58.504 45.455 0.00 0.00 0.00 2.74
3282 6218 0.249911 GCTTCGTGTTGACTCCACCT 60.250 55.000 0.00 0.00 0.00 4.00
3330 6266 0.987294 CCTCATTATCCCGGATGGCT 59.013 55.000 10.45 0.00 0.00 4.75
3384 6320 1.548719 TGGTTGACCTGATCGAACGAT 59.451 47.619 9.46 9.46 35.67 3.73
3390 6326 0.460109 TCGCATGGTTGACCTGATCG 60.460 55.000 1.34 0.98 36.82 3.69
3408 6344 2.095364 CAGCTCTTTCACCATTGCACTC 60.095 50.000 0.00 0.00 0.00 3.51
3489 6431 2.858974 CTTCCCCCACCACCACCT 60.859 66.667 0.00 0.00 0.00 4.00
3579 6521 1.337167 CGCAGTTCACTCTCACCATGA 60.337 52.381 0.00 0.00 0.00 3.07
3686 6628 2.605607 CCATGGGTGAGTGGCCTCA 61.606 63.158 2.85 0.00 45.44 3.86
3694 6636 2.362736 CTCAACATGACCATGGGTGAG 58.637 52.381 18.09 21.02 42.82 3.51
3761 6703 1.160137 ACAGCGAGCTGATCAAAACC 58.840 50.000 29.11 0.00 46.30 3.27
3763 6705 3.433274 CAGTTACAGCGAGCTGATCAAAA 59.567 43.478 29.11 12.84 46.30 2.44
3765 6707 2.231235 TCAGTTACAGCGAGCTGATCAA 59.769 45.455 29.11 16.79 46.30 2.57
3852 6794 1.565067 TGGATGCAGAGCAGAGAGAA 58.435 50.000 0.00 0.00 43.65 2.87
3864 6806 6.815089 AGAAACAGTACAAAAATTGGATGCA 58.185 32.000 0.00 0.00 34.12 3.96
4037 6986 9.913310 ATTGTCAAAAATTAAAGGGAAAAAGGA 57.087 25.926 0.00 0.00 0.00 3.36
4045 6997 9.981114 AGTAGTTCATTGTCAAAAATTAAAGGG 57.019 29.630 0.00 0.00 0.00 3.95
4075 7032 6.371809 TCTTATTGTATCCAAACCGAATGC 57.628 37.500 0.00 0.00 33.44 3.56
4196 7155 1.362355 CGTTTGGGTGAGGCAAACC 59.638 57.895 0.00 0.19 35.95 3.27
4200 7159 2.203280 CCACGTTTGGGTGAGGCA 60.203 61.111 0.00 0.00 40.38 4.75
4216 7206 4.767255 CTCTCTGGCGGCACCACC 62.767 72.222 7.97 0.00 46.36 4.61
4260 7269 0.679505 CACTCGTCTGGACAAAGGGA 59.320 55.000 1.63 0.00 0.00 4.20
4298 7307 9.692749 CATCCAGCGAAAAATATACTTCTACTA 57.307 33.333 0.00 0.00 0.00 1.82
4303 7312 7.920738 AGAACATCCAGCGAAAAATATACTTC 58.079 34.615 0.00 0.00 0.00 3.01
4312 7321 2.552315 GACCAAGAACATCCAGCGAAAA 59.448 45.455 0.00 0.00 0.00 2.29
4317 7326 2.191128 ACTGACCAAGAACATCCAGC 57.809 50.000 0.00 0.00 0.00 4.85
4355 7364 6.651225 GCTTGATTAGATACCCTGAACATACC 59.349 42.308 0.00 0.00 0.00 2.73
4357 7366 7.373617 TGCTTGATTAGATACCCTGAACATA 57.626 36.000 0.00 0.00 0.00 2.29
4358 7367 6.252599 TGCTTGATTAGATACCCTGAACAT 57.747 37.500 0.00 0.00 0.00 2.71
4359 7368 5.674525 CTGCTTGATTAGATACCCTGAACA 58.325 41.667 0.00 0.00 0.00 3.18
4360 7369 4.513318 GCTGCTTGATTAGATACCCTGAAC 59.487 45.833 0.00 0.00 0.00 3.18
4361 7370 4.410228 AGCTGCTTGATTAGATACCCTGAA 59.590 41.667 0.00 0.00 0.00 3.02
4362 7371 3.969976 AGCTGCTTGATTAGATACCCTGA 59.030 43.478 0.00 0.00 0.00 3.86
4363 7372 4.063689 CAGCTGCTTGATTAGATACCCTG 58.936 47.826 0.00 0.00 0.00 4.45
4364 7373 3.969976 TCAGCTGCTTGATTAGATACCCT 59.030 43.478 9.47 0.00 0.00 4.34
4365 7374 4.342862 TCAGCTGCTTGATTAGATACCC 57.657 45.455 9.47 0.00 0.00 3.69
4366 7375 5.277731 GCTTTCAGCTGCTTGATTAGATACC 60.278 44.000 9.47 0.00 38.45 2.73
4367 7376 5.295292 TGCTTTCAGCTGCTTGATTAGATAC 59.705 40.000 9.47 0.00 42.97 2.24
4368 7377 5.430886 TGCTTTCAGCTGCTTGATTAGATA 58.569 37.500 9.47 0.00 42.97 1.98
4369 7378 4.267536 TGCTTTCAGCTGCTTGATTAGAT 58.732 39.130 9.47 0.00 42.97 1.98
4370 7379 3.678289 TGCTTTCAGCTGCTTGATTAGA 58.322 40.909 9.47 0.00 42.97 2.10
4371 7380 4.634184 ATGCTTTCAGCTGCTTGATTAG 57.366 40.909 9.47 3.94 42.97 1.73
4395 7404 3.990469 CCTGGCTCGTTATTATACAGCTG 59.010 47.826 13.48 13.48 0.00 4.24
4442 7451 3.569701 CAGTGTTGGTTTACTGCTGGATT 59.430 43.478 0.00 0.00 38.01 3.01
4443 7452 3.149196 CAGTGTTGGTTTACTGCTGGAT 58.851 45.455 0.00 0.00 38.01 3.41
4444 7453 2.571212 CAGTGTTGGTTTACTGCTGGA 58.429 47.619 0.00 0.00 38.01 3.86
4500 7509 5.535333 TGCTGTGTAAGTGTAAAGTAGTCC 58.465 41.667 0.00 0.00 0.00 3.85
4508 7517 6.000840 TGATTTGGATGCTGTGTAAGTGTAA 58.999 36.000 0.00 0.00 0.00 2.41
4509 7518 5.555966 TGATTTGGATGCTGTGTAAGTGTA 58.444 37.500 0.00 0.00 0.00 2.90
4510 7519 4.397420 TGATTTGGATGCTGTGTAAGTGT 58.603 39.130 0.00 0.00 0.00 3.55
4511 7520 5.571784 ATGATTTGGATGCTGTGTAAGTG 57.428 39.130 0.00 0.00 0.00 3.16
4512 7521 6.653020 TCTATGATTTGGATGCTGTGTAAGT 58.347 36.000 0.00 0.00 0.00 2.24
4513 7522 7.660617 AGATCTATGATTTGGATGCTGTGTAAG 59.339 37.037 0.00 0.00 0.00 2.34
4535 7544 1.077429 GGGTGGGCAAGTCCAGATC 60.077 63.158 0.00 0.00 37.50 2.75
4578 7590 3.181474 GCTTTATCCGACTGACCTAGCTT 60.181 47.826 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.