Multiple sequence alignment - TraesCS1A01G036000

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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 TraesCS1A01G036000 chr1A 100.000 4756 0 0 1 4756 20031993 20027238 0.000000e+00 8783.0
1 TraesCS1A01G036000 chr1A 86.364 264 31 3 1702 1964 20027858 20027599 2.800000e-72 283.0
2 TraesCS1A01G036000 chr1A 86.364 264 31 3 4136 4395 20030292 20030030 2.800000e-72 283.0
3 TraesCS1A01G036000 chr1A 91.597 119 8 2 388 505 33228007 33227890 3.810000e-36 163.0
4 TraesCS1A01G036000 chr1B 96.594 3611 108 10 1153 4756 26395168 26398770 0.000000e+00 5973.0
5 TraesCS1A01G036000 chr1B 96.590 1525 47 4 3234 4756 26402274 26403795 0.000000e+00 2523.0
6 TraesCS1A01G036000 chr1B 82.825 1246 138 35 2855 4054 26404466 26405681 0.000000e+00 1046.0
7 TraesCS1A01G036000 chr1B 90.466 472 31 6 691 1153 26394657 26395123 1.130000e-170 610.0
8 TraesCS1A01G036000 chr1B 86.164 477 58 5 2326 2797 26398956 26399429 4.250000e-140 508.0
9 TraesCS1A01G036000 chr1B 85.954 477 59 5 2326 2797 26403981 26404454 1.980000e-138 503.0
10 TraesCS1A01G036000 chr1B 84.760 479 39 15 3503 3965 26400056 26400516 2.610000e-122 449.0
11 TraesCS1A01G036000 chr1B 87.072 263 31 1 1702 1964 26398150 26398409 1.290000e-75 294.0
12 TraesCS1A01G036000 chr1B 82.883 333 49 6 67 394 26394092 26394421 4.660000e-75 292.0
13 TraesCS1A01G036000 chr1B 86.692 263 32 1 1702 1964 26403175 26403434 6.020000e-74 289.0
14 TraesCS1A01G036000 chr1B 90.233 215 15 2 495 707 26394425 26394635 4.690000e-70 276.0
15 TraesCS1A01G036000 chr1D 90.435 4161 236 57 665 4756 18001153 17997086 0.000000e+00 5330.0
16 TraesCS1A01G036000 chr1D 86.101 1072 114 21 2326 3389 17996898 17995854 0.000000e+00 1122.0
17 TraesCS1A01G036000 chr1D 90.090 333 33 0 1982 2314 17997471 17997139 2.630000e-117 433.0
18 TraesCS1A01G036000 chr1D 87.963 324 36 1 4374 4694 17999856 17999533 3.470000e-101 379.0
19 TraesCS1A01G036000 chr1D 80.846 402 60 14 4 394 412744887 412745282 2.780000e-77 300.0
20 TraesCS1A01G036000 chr1D 80.846 402 60 14 4 394 412762226 412762621 2.780000e-77 300.0
21 TraesCS1A01G036000 chr1D 87.405 262 30 1 1703 1964 17997708 17997450 1.000000e-76 298.0
22 TraesCS1A01G036000 chr1D 79.449 399 70 11 7 394 412640910 412641307 6.060000e-69 272.0
23 TraesCS1A01G036000 chr1D 95.370 108 3 2 399 505 315817006 315816900 2.280000e-38 171.0
24 TraesCS1A01G036000 chr1D 94.545 110 5 1 400 508 314718404 314718513 8.190000e-38 169.0
25 TraesCS1A01G036000 chr1D 94.000 50 3 0 3524 3573 17995814 17995765 5.100000e-10 76.8
26 TraesCS1A01G036000 chrUn 85.856 403 39 10 1 401 458005675 458005289 3.420000e-111 412.0
27 TraesCS1A01G036000 chr2A 80.800 250 39 7 154 396 771076545 771076298 2.260000e-43 187.0
28 TraesCS1A01G036000 chr6B 96.262 107 4 0 398 504 718346809 718346915 4.890000e-40 176.0
29 TraesCS1A01G036000 chr3B 97.115 104 3 0 398 501 560117297 560117400 4.890000e-40 176.0
30 TraesCS1A01G036000 chr3B 95.413 109 5 0 397 505 719044010 719044118 1.760000e-39 174.0
31 TraesCS1A01G036000 chr3B 95.370 108 5 0 394 501 5951435 5951328 6.330000e-39 172.0
32 TraesCS1A01G036000 chr7D 95.327 107 5 0 396 502 386385218 386385324 2.280000e-38 171.0
33 TraesCS1A01G036000 chr6A 95.327 107 5 0 399 505 315625263 315625369 2.280000e-38 171.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G036000 chr1A 20027238 20031993 4755 True 8783.000000 8783 100.000000 1 4756 1 chr1A.!!$R1 4755
1 TraesCS1A01G036000 chr1A 20027599 20030292 2693 True 283.000000 283 86.364000 1702 4395 2 chr1A.!!$R3 2693
2 TraesCS1A01G036000 chr1B 26394092 26405681 11589 False 1160.272727 5973 88.203000 67 4756 11 chr1B.!!$F1 4689
3 TraesCS1A01G036000 chr1D 17995765 18001153 5388 True 2176.266667 5330 90.178667 665 4756 3 chr1D.!!$R2 4091
4 TraesCS1A01G036000 chr1D 17997139 17999856 2717 True 370.000000 433 88.486000 1703 4694 3 chr1D.!!$R3 2991

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
419 424 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.0 0.00 0.0 0.00 3.46 F
1458 1556 0.476771 ACCACGAGGACCACCAAATT 59.523 50.0 5.68 0.0 38.69 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1719 0.458543 AAGTAGTGCGCCGATGACTG 60.459 55.0 4.18 0.0 0.0 3.51 R
4668 9861 5.880332 TGCTTACTACATTGGAACTTGATCC 59.120 40.0 0.00 0.0 40.1 3.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.489938 GGGCCTACATGTCAAGTCAA 57.510 50.000 0.00 0.00 0.00 3.18
20 21 2.790433 GGGCCTACATGTCAAGTCAAA 58.210 47.619 0.00 0.00 0.00 2.69
21 22 3.153919 GGGCCTACATGTCAAGTCAAAA 58.846 45.455 0.00 0.00 0.00 2.44
22 23 3.763897 GGGCCTACATGTCAAGTCAAAAT 59.236 43.478 0.00 0.00 0.00 1.82
23 24 4.380867 GGGCCTACATGTCAAGTCAAAATG 60.381 45.833 0.00 0.00 0.00 2.32
24 25 4.218417 GGCCTACATGTCAAGTCAAAATGT 59.782 41.667 0.00 0.00 35.70 2.71
25 26 5.278957 GGCCTACATGTCAAGTCAAAATGTT 60.279 40.000 0.00 0.00 33.67 2.71
26 27 6.215845 GCCTACATGTCAAGTCAAAATGTTT 58.784 36.000 0.00 0.00 33.67 2.83
27 28 6.363357 GCCTACATGTCAAGTCAAAATGTTTC 59.637 38.462 0.00 0.00 33.67 2.78
28 29 7.424803 CCTACATGTCAAGTCAAAATGTTTCA 58.575 34.615 0.00 0.00 33.67 2.69
29 30 7.592533 CCTACATGTCAAGTCAAAATGTTTCAG 59.407 37.037 0.00 0.00 33.67 3.02
30 31 7.099266 ACATGTCAAGTCAAAATGTTTCAGA 57.901 32.000 0.00 0.00 0.00 3.27
31 32 6.974622 ACATGTCAAGTCAAAATGTTTCAGAC 59.025 34.615 0.00 0.00 0.00 3.51
32 33 6.507958 TGTCAAGTCAAAATGTTTCAGACA 57.492 33.333 11.22 0.00 43.71 3.41
33 34 6.918626 TGTCAAGTCAAAATGTTTCAGACAA 58.081 32.000 11.22 0.00 42.62 3.18
34 35 6.806249 TGTCAAGTCAAAATGTTTCAGACAAC 59.194 34.615 11.22 8.01 42.62 3.32
35 36 6.021468 GTCAAGTCAAAATGTTTCAGACAACG 60.021 38.462 11.22 0.00 42.62 4.10
36 37 4.920376 AGTCAAAATGTTTCAGACAACGG 58.080 39.130 11.22 0.00 42.62 4.44
37 38 4.398044 AGTCAAAATGTTTCAGACAACGGT 59.602 37.500 11.22 0.00 42.62 4.83
38 39 4.499040 GTCAAAATGTTTCAGACAACGGTG 59.501 41.667 0.00 0.00 42.62 4.94
39 40 3.708563 AAATGTTTCAGACAACGGTGG 57.291 42.857 4.97 0.00 42.62 4.61
40 41 1.604604 ATGTTTCAGACAACGGTGGG 58.395 50.000 4.97 0.00 42.62 4.61
41 42 0.542333 TGTTTCAGACAACGGTGGGA 59.458 50.000 4.97 0.00 34.69 4.37
42 43 1.142060 TGTTTCAGACAACGGTGGGAT 59.858 47.619 4.97 0.00 34.69 3.85
43 44 1.535462 GTTTCAGACAACGGTGGGATG 59.465 52.381 4.97 0.00 0.00 3.51
44 45 0.605319 TTCAGACAACGGTGGGATGC 60.605 55.000 4.97 0.00 0.00 3.91
45 46 2.040544 CAGACAACGGTGGGATGCC 61.041 63.158 4.97 0.00 0.00 4.40
61 62 2.651361 CCGAGCGGGCCTGTATAG 59.349 66.667 14.55 2.74 0.00 1.31
62 63 2.049063 CGAGCGGGCCTGTATAGC 60.049 66.667 14.55 4.67 0.00 2.97
63 64 2.565645 CGAGCGGGCCTGTATAGCT 61.566 63.158 14.55 9.57 41.29 3.32
64 65 1.290639 GAGCGGGCCTGTATAGCTC 59.709 63.158 14.55 12.11 45.74 4.09
65 66 1.152440 AGCGGGCCTGTATAGCTCT 60.152 57.895 14.55 0.00 31.94 4.09
66 67 1.182385 AGCGGGCCTGTATAGCTCTC 61.182 60.000 14.55 0.00 31.94 3.20
67 68 1.581954 CGGGCCTGTATAGCTCTCG 59.418 63.158 2.29 0.00 0.00 4.04
68 69 1.867919 CGGGCCTGTATAGCTCTCGG 61.868 65.000 2.29 0.00 0.00 4.63
69 70 1.536943 GGGCCTGTATAGCTCTCGGG 61.537 65.000 0.84 0.00 0.00 5.14
70 71 0.539901 GGCCTGTATAGCTCTCGGGA 60.540 60.000 12.78 0.00 0.00 5.14
71 72 1.329256 GCCTGTATAGCTCTCGGGAA 58.671 55.000 12.78 0.00 0.00 3.97
134 137 8.451687 TTCAAATGATTAGAAATGTTTCAGCG 57.548 30.769 8.09 0.00 39.61 5.18
138 141 6.741992 TGATTAGAAATGTTTCAGCGACAT 57.258 33.333 8.09 0.00 39.61 3.06
139 142 6.545508 TGATTAGAAATGTTTCAGCGACATG 58.454 36.000 8.09 0.00 37.76 3.21
143 146 1.167851 ATGTTTCAGCGACATGTGGG 58.832 50.000 1.15 0.00 36.43 4.61
150 153 0.908910 AGCGACATGTGGGTCCAATA 59.091 50.000 1.15 0.00 34.24 1.90
152 155 1.134521 GCGACATGTGGGTCCAATAGA 60.135 52.381 1.15 0.00 34.24 1.98
180 183 1.464997 GTCAGGTCAGAATGTTTCGGC 59.535 52.381 0.00 0.00 37.40 5.54
185 188 1.732259 GTCAGAATGTTTCGGCGACAT 59.268 47.619 10.16 9.00 39.31 3.06
198 201 2.436646 GACATGTGGGGTGCCGAG 60.437 66.667 1.15 0.00 0.00 4.63
199 202 4.722700 ACATGTGGGGTGCCGAGC 62.723 66.667 0.00 0.00 0.00 5.03
254 259 1.091771 CGGAGCCGTCAGATGCAAAT 61.092 55.000 0.00 0.00 34.35 2.32
259 264 1.452110 CCGTCAGATGCAAATGGACA 58.548 50.000 0.00 0.00 0.00 4.02
260 265 2.019249 CCGTCAGATGCAAATGGACAT 58.981 47.619 0.00 0.00 0.00 3.06
263 268 1.402613 TCAGATGCAAATGGACATGCG 59.597 47.619 0.00 0.00 45.47 4.73
269 274 1.132834 GCAAATGGACATGCGACATGA 59.867 47.619 21.37 4.98 32.17 3.07
271 276 2.112380 AATGGACATGCGACATGACA 57.888 45.000 21.37 18.67 0.00 3.58
281 286 2.005451 GCGACATGACATCTCTTTGCT 58.995 47.619 0.00 0.00 0.00 3.91
282 287 3.190079 GCGACATGACATCTCTTTGCTA 58.810 45.455 0.00 0.00 0.00 3.49
286 291 5.276726 CGACATGACATCTCTTTGCTATGTG 60.277 44.000 0.00 0.00 34.09 3.21
288 293 4.824479 TGACATCTCTTTGCTATGTGGA 57.176 40.909 0.00 0.00 34.09 4.02
289 294 5.363562 TGACATCTCTTTGCTATGTGGAT 57.636 39.130 0.00 0.00 34.09 3.41
298 303 0.387878 GCTATGTGGATCTCTCGGCG 60.388 60.000 0.00 0.00 0.00 6.46
329 334 1.301716 GCCGACTGTGCCTTCTTCA 60.302 57.895 0.00 0.00 0.00 3.02
332 337 1.284982 CGACTGTGCCTTCTTCACCG 61.285 60.000 0.00 0.00 33.71 4.94
342 347 2.224066 CCTTCTTCACCGTGTCTTCTGT 60.224 50.000 0.00 0.00 0.00 3.41
343 348 2.509052 TCTTCACCGTGTCTTCTGTG 57.491 50.000 0.00 0.00 0.00 3.66
345 350 0.176910 TTCACCGTGTCTTCTGTGCA 59.823 50.000 0.00 0.00 0.00 4.57
347 352 0.249447 CACCGTGTCTTCTGTGCAGA 60.249 55.000 0.00 0.00 35.27 4.26
348 353 0.464036 ACCGTGTCTTCTGTGCAGAA 59.536 50.000 13.22 13.22 44.47 3.02
349 354 1.134521 ACCGTGTCTTCTGTGCAGAAA 60.135 47.619 14.54 4.89 45.75 2.52
350 355 2.146342 CCGTGTCTTCTGTGCAGAAAT 58.854 47.619 14.54 0.00 45.75 2.17
363 368 5.221880 TGTGCAGAAATAACATCTTGTTGC 58.778 37.500 3.22 0.00 41.30 4.17
384 389 1.305201 GTGTCCTTGTCTTTGCCGAA 58.695 50.000 0.00 0.00 0.00 4.30
387 392 3.071479 TGTCCTTGTCTTTGCCGAATAC 58.929 45.455 0.00 0.00 0.00 1.89
394 399 5.401531 TGTCTTTGCCGAATACTACTCTT 57.598 39.130 0.00 0.00 0.00 2.85
397 402 5.288952 GTCTTTGCCGAATACTACTCTTGTC 59.711 44.000 0.00 0.00 0.00 3.18
398 403 4.794278 TTGCCGAATACTACTCTTGTCA 57.206 40.909 0.00 0.00 0.00 3.58
401 406 6.650427 TGCCGAATACTACTCTTGTCATAT 57.350 37.500 0.00 0.00 0.00 1.78
402 407 7.754851 TGCCGAATACTACTCTTGTCATATA 57.245 36.000 0.00 0.00 0.00 0.86
403 408 7.591165 TGCCGAATACTACTCTTGTCATATAC 58.409 38.462 0.00 0.00 0.00 1.47
404 409 7.447545 TGCCGAATACTACTCTTGTCATATACT 59.552 37.037 0.00 0.00 0.00 2.12
405 410 7.964011 GCCGAATACTACTCTTGTCATATACTC 59.036 40.741 0.00 0.00 0.00 2.59
406 411 8.452534 CCGAATACTACTCTTGTCATATACTCC 58.547 40.741 0.00 0.00 0.00 3.85
407 412 8.452534 CGAATACTACTCTTGTCATATACTCCC 58.547 40.741 0.00 0.00 0.00 4.30
408 413 9.523168 GAATACTACTCTTGTCATATACTCCCT 57.477 37.037 0.00 0.00 0.00 4.20
409 414 9.523168 AATACTACTCTTGTCATATACTCCCTC 57.477 37.037 0.00 0.00 0.00 4.30
410 415 6.308566 ACTACTCTTGTCATATACTCCCTCC 58.691 44.000 0.00 0.00 0.00 4.30
411 416 4.145807 ACTCTTGTCATATACTCCCTCCG 58.854 47.826 0.00 0.00 0.00 4.63
412 417 4.145807 CTCTTGTCATATACTCCCTCCGT 58.854 47.826 0.00 0.00 0.00 4.69
413 418 4.142790 TCTTGTCATATACTCCCTCCGTC 58.857 47.826 0.00 0.00 0.00 4.79
414 419 2.872732 TGTCATATACTCCCTCCGTCC 58.127 52.381 0.00 0.00 0.00 4.79
415 420 2.169330 GTCATATACTCCCTCCGTCCC 58.831 57.143 0.00 0.00 0.00 4.46
416 421 1.174783 CATATACTCCCTCCGTCCCG 58.825 60.000 0.00 0.00 0.00 5.14
417 422 1.070604 ATATACTCCCTCCGTCCCGA 58.929 55.000 0.00 0.00 0.00 5.14
418 423 0.846015 TATACTCCCTCCGTCCCGAA 59.154 55.000 0.00 0.00 0.00 4.30
419 424 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
420 425 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
421 426 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
422 427 1.117150 CTCCCTCCGTCCCGAAATAA 58.883 55.000 0.00 0.00 0.00 1.40
423 428 1.068741 CTCCCTCCGTCCCGAAATAAG 59.931 57.143 0.00 0.00 0.00 1.73
424 429 0.828677 CCCTCCGTCCCGAAATAAGT 59.171 55.000 0.00 0.00 0.00 2.24
425 430 1.472728 CCCTCCGTCCCGAAATAAGTG 60.473 57.143 0.00 0.00 0.00 3.16
426 431 1.206371 CCTCCGTCCCGAAATAAGTGT 59.794 52.381 0.00 0.00 0.00 3.55
427 432 2.537401 CTCCGTCCCGAAATAAGTGTC 58.463 52.381 0.00 0.00 0.00 3.67
428 433 2.165845 CTCCGTCCCGAAATAAGTGTCT 59.834 50.000 0.00 0.00 0.00 3.41
429 434 2.165030 TCCGTCCCGAAATAAGTGTCTC 59.835 50.000 0.00 0.00 0.00 3.36
430 435 2.094390 CCGTCCCGAAATAAGTGTCTCA 60.094 50.000 0.00 0.00 0.00 3.27
431 436 3.581755 CGTCCCGAAATAAGTGTCTCAA 58.418 45.455 0.00 0.00 0.00 3.02
432 437 3.367025 CGTCCCGAAATAAGTGTCTCAAC 59.633 47.826 0.00 0.00 0.00 3.18
433 438 4.566987 GTCCCGAAATAAGTGTCTCAACT 58.433 43.478 0.00 0.00 0.00 3.16
434 439 4.995487 GTCCCGAAATAAGTGTCTCAACTT 59.005 41.667 0.00 0.00 42.89 2.66
435 440 5.469084 GTCCCGAAATAAGTGTCTCAACTTT 59.531 40.000 0.00 0.00 40.77 2.66
436 441 5.468746 TCCCGAAATAAGTGTCTCAACTTTG 59.531 40.000 0.00 0.00 40.77 2.77
437 442 5.238650 CCCGAAATAAGTGTCTCAACTTTGT 59.761 40.000 0.00 0.00 40.77 2.83
438 443 6.425721 CCCGAAATAAGTGTCTCAACTTTGTA 59.574 38.462 0.00 0.00 40.77 2.41
439 444 7.288672 CCGAAATAAGTGTCTCAACTTTGTAC 58.711 38.462 0.00 0.00 40.77 2.90
440 445 7.170998 CCGAAATAAGTGTCTCAACTTTGTACT 59.829 37.037 0.00 0.00 40.77 2.73
441 446 9.188588 CGAAATAAGTGTCTCAACTTTGTACTA 57.811 33.333 0.00 0.00 40.77 1.82
443 448 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
444 449 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
445 450 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
446 451 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
447 452 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
448 453 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
450 455 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
451 456 8.895737 GTCTCAACTTTGTACTAGCTCTAGTAT 58.104 37.037 16.96 1.87 46.57 2.12
476 481 9.726438 ATAAATTTGTACTAAGCTCAAGACACT 57.274 29.630 0.00 0.00 0.00 3.55
477 482 8.451908 AAATTTGTACTAAGCTCAAGACACTT 57.548 30.769 3.19 0.00 0.00 3.16
478 483 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
479 484 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
480 485 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
481 486 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
482 487 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
483 488 9.555727 TGTACTAAGCTCAAGACACTTATTTTT 57.444 29.630 3.19 0.00 0.00 1.94
484 489 9.813080 GTACTAAGCTCAAGACACTTATTTTTG 57.187 33.333 3.19 0.00 0.00 2.44
485 490 7.875971 ACTAAGCTCAAGACACTTATTTTTGG 58.124 34.615 3.19 0.00 0.00 3.28
486 491 6.959639 AAGCTCAAGACACTTATTTTTGGA 57.040 33.333 0.00 0.00 0.00 3.53
487 492 6.319141 AGCTCAAGACACTTATTTTTGGAC 57.681 37.500 0.00 0.00 0.00 4.02
488 493 5.049405 AGCTCAAGACACTTATTTTTGGACG 60.049 40.000 0.00 0.00 0.00 4.79
489 494 5.682943 TCAAGACACTTATTTTTGGACGG 57.317 39.130 0.00 0.00 0.00 4.79
490 495 5.369833 TCAAGACACTTATTTTTGGACGGA 58.630 37.500 0.00 0.00 0.00 4.69
491 496 5.468746 TCAAGACACTTATTTTTGGACGGAG 59.531 40.000 0.00 0.00 0.00 4.63
492 497 4.324267 AGACACTTATTTTTGGACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
493 498 3.418047 ACACTTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
494 499 3.073356 ACACTTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
495 500 3.689649 CACTTATTTTTGGACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
499 504 6.384886 ACTTATTTTTGGACGGAGGGAGTATA 59.615 38.462 0.00 0.00 0.00 1.47
530 535 3.302344 CCCGTGGTTTGGCCCTTG 61.302 66.667 0.00 0.00 36.04 3.61
532 537 3.302344 CGTGGTTTGGCCCTTGGG 61.302 66.667 0.00 0.32 36.04 4.12
555 560 3.116531 GCCCAACACTCGGCGTAC 61.117 66.667 6.85 0.00 34.94 3.67
565 570 1.073177 CTCGGCGTACGGTGAAATTT 58.927 50.000 18.39 0.00 44.45 1.82
571 576 3.061697 GGCGTACGGTGAAATTTCAGTAG 59.938 47.826 21.05 16.27 37.98 2.57
572 577 3.676646 GCGTACGGTGAAATTTCAGTAGT 59.323 43.478 21.05 20.40 37.98 2.73
574 579 4.682860 CGTACGGTGAAATTTCAGTAGTGT 59.317 41.667 21.05 15.75 37.98 3.55
618 623 2.224450 ACCCACGGAGGAGTGTAAAAAG 60.224 50.000 0.00 0.00 41.22 2.27
643 648 1.659098 GTAGGTGGCTGTCGATTTTCG 59.341 52.381 0.00 0.00 42.10 3.46
647 652 1.933853 GTGGCTGTCGATTTTCGCTAT 59.066 47.619 0.00 0.00 40.21 2.97
648 653 2.033662 GTGGCTGTCGATTTTCGCTATC 60.034 50.000 0.00 0.00 40.21 2.08
649 654 2.201732 GGCTGTCGATTTTCGCTATCA 58.798 47.619 0.00 0.00 40.21 2.15
650 655 2.607635 GGCTGTCGATTTTCGCTATCAA 59.392 45.455 0.00 0.00 40.21 2.57
656 661 3.876914 TCGATTTTCGCTATCAAATGGCT 59.123 39.130 0.00 0.00 40.21 4.75
762 809 2.032528 TGCTCCAACCGCCAGAAG 59.967 61.111 0.00 0.00 0.00 2.85
787 834 3.436055 AGAGCGCGCGAACTCTCT 61.436 61.111 37.18 30.15 38.98 3.10
794 841 1.136984 CGCGAACTCTCTAACCGCT 59.863 57.895 0.00 0.00 43.19 5.52
904 953 4.111016 CACCGTGTAGAGCCGCGA 62.111 66.667 8.23 0.00 40.64 5.87
911 960 3.370231 TAGAGCCGCGACAGTGCA 61.370 61.111 8.23 0.00 34.15 4.57
928 977 4.197107 GTGCACTTCACACAGTTAGTTC 57.803 45.455 10.32 0.00 44.98 3.01
930 979 3.202906 GCACTTCACACAGTTAGTTCCA 58.797 45.455 0.00 0.00 0.00 3.53
931 980 3.002348 GCACTTCACACAGTTAGTTCCAC 59.998 47.826 0.00 0.00 0.00 4.02
933 982 2.519377 TCACACAGTTAGTTCCACCG 57.481 50.000 0.00 0.00 0.00 4.94
934 983 0.865769 CACACAGTTAGTTCCACCGC 59.134 55.000 0.00 0.00 0.00 5.68
936 985 1.005394 ACAGTTAGTTCCACCGCCG 60.005 57.895 0.00 0.00 0.00 6.46
937 986 1.005394 CAGTTAGTTCCACCGCCGT 60.005 57.895 0.00 0.00 0.00 5.68
939 988 0.601841 AGTTAGTTCCACCGCCGTTG 60.602 55.000 0.00 0.00 0.00 4.10
940 989 1.962306 TTAGTTCCACCGCCGTTGC 60.962 57.895 0.00 0.00 0.00 4.17
942 991 2.775032 TAGTTCCACCGCCGTTGCTC 62.775 60.000 0.00 0.00 34.43 4.26
951 1001 2.266055 CCGTTGCTCCCTCCACTC 59.734 66.667 0.00 0.00 0.00 3.51
956 1006 3.403558 GCTCCCTCCACTCCACCC 61.404 72.222 0.00 0.00 0.00 4.61
974 1024 3.121030 GCACATTCGCCAGCGTCT 61.121 61.111 12.32 0.00 40.74 4.18
982 1032 4.112341 GCCAGCGTCTACGTCCGT 62.112 66.667 4.24 0.00 42.22 4.69
1134 1184 1.535204 CCCAACACCAACAGGATGCC 61.535 60.000 0.00 0.00 42.53 4.40
1306 1404 2.422519 CCCATCCCTCAAGTTCATCCAG 60.423 54.545 0.00 0.00 0.00 3.86
1399 1497 2.874701 GAGCACGATCAATACCAGCATT 59.125 45.455 0.00 0.00 0.00 3.56
1458 1556 0.476771 ACCACGAGGACCACCAAATT 59.523 50.000 5.68 0.00 38.69 1.82
1608 1706 4.178169 ACGGCCGTCCAACACCAA 62.178 61.111 28.70 0.00 0.00 3.67
1621 1719 1.741770 CACCAACAGACGCTAGGCC 60.742 63.158 0.00 0.00 0.00 5.19
1641 1739 0.458543 AGTCATCGGCGCACTACTTG 60.459 55.000 10.83 0.00 0.00 3.16
4478 9668 4.478686 ACCAGGAATACATTCTTAGCCCTT 59.521 41.667 0.00 0.00 37.00 3.95
4546 9736 8.327429 CAAAATGACCAATTTAATATTGCCGAC 58.673 33.333 0.00 0.00 37.51 4.79
4724 9917 2.355132 GTCTGACCGATCGTACTCATGT 59.645 50.000 15.09 2.21 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.424803 TGAAACATTTTGACTTGACATGTAGG 58.575 34.615 0.00 0.00 0.00 3.18
6 7 6.974622 GTCTGAAACATTTTGACTTGACATGT 59.025 34.615 0.00 0.00 0.00 3.21
7 8 6.974048 TGTCTGAAACATTTTGACTTGACATG 59.026 34.615 0.00 0.00 31.20 3.21
8 9 7.099266 TGTCTGAAACATTTTGACTTGACAT 57.901 32.000 10.58 0.00 31.20 3.06
9 10 6.507958 TGTCTGAAACATTTTGACTTGACA 57.492 33.333 10.58 0.00 31.20 3.58
10 11 6.021468 CGTTGTCTGAAACATTTTGACTTGAC 60.021 38.462 10.58 0.00 37.82 3.18
11 12 6.027131 CGTTGTCTGAAACATTTTGACTTGA 58.973 36.000 10.58 0.00 37.82 3.02
12 13 5.229887 CCGTTGTCTGAAACATTTTGACTTG 59.770 40.000 10.58 0.00 37.82 3.16
13 14 5.105917 ACCGTTGTCTGAAACATTTTGACTT 60.106 36.000 10.58 0.00 37.82 3.01
14 15 4.398044 ACCGTTGTCTGAAACATTTTGACT 59.602 37.500 10.58 0.00 37.82 3.41
15 16 4.499040 CACCGTTGTCTGAAACATTTTGAC 59.501 41.667 0.00 0.00 37.82 3.18
16 17 4.439426 CCACCGTTGTCTGAAACATTTTGA 60.439 41.667 0.00 0.00 37.82 2.69
17 18 3.796178 CCACCGTTGTCTGAAACATTTTG 59.204 43.478 0.00 0.00 37.82 2.44
18 19 3.181480 CCCACCGTTGTCTGAAACATTTT 60.181 43.478 0.00 0.00 37.82 1.82
19 20 2.360801 CCCACCGTTGTCTGAAACATTT 59.639 45.455 0.00 0.00 37.82 2.32
20 21 1.953686 CCCACCGTTGTCTGAAACATT 59.046 47.619 0.00 0.00 37.82 2.71
21 22 1.142060 TCCCACCGTTGTCTGAAACAT 59.858 47.619 0.00 0.00 37.82 2.71
22 23 0.542333 TCCCACCGTTGTCTGAAACA 59.458 50.000 0.00 0.00 35.59 2.83
23 24 1.535462 CATCCCACCGTTGTCTGAAAC 59.465 52.381 0.00 0.00 0.00 2.78
24 25 1.890876 CATCCCACCGTTGTCTGAAA 58.109 50.000 0.00 0.00 0.00 2.69
25 26 0.605319 GCATCCCACCGTTGTCTGAA 60.605 55.000 0.00 0.00 0.00 3.02
26 27 1.003839 GCATCCCACCGTTGTCTGA 60.004 57.895 0.00 0.00 0.00 3.27
27 28 2.040544 GGCATCCCACCGTTGTCTG 61.041 63.158 0.00 0.00 0.00 3.51
28 29 2.351276 GGCATCCCACCGTTGTCT 59.649 61.111 0.00 0.00 0.00 3.41
29 30 3.124921 CGGCATCCCACCGTTGTC 61.125 66.667 0.00 0.00 45.70 3.18
44 45 2.651361 CTATACAGGCCCGCTCGG 59.349 66.667 0.00 0.48 0.00 4.63
45 46 2.049063 GCTATACAGGCCCGCTCG 60.049 66.667 0.00 0.00 0.00 5.03
46 47 1.182385 AGAGCTATACAGGCCCGCTC 61.182 60.000 0.00 7.86 45.49 5.03
47 48 1.152440 AGAGCTATACAGGCCCGCT 60.152 57.895 0.00 0.00 0.00 5.52
48 49 1.290639 GAGAGCTATACAGGCCCGC 59.709 63.158 0.00 0.00 0.00 6.13
49 50 1.581954 CGAGAGCTATACAGGCCCG 59.418 63.158 0.00 0.00 0.00 6.13
50 51 1.536943 CCCGAGAGCTATACAGGCCC 61.537 65.000 0.00 0.00 0.00 5.80
51 52 0.539901 TCCCGAGAGCTATACAGGCC 60.540 60.000 0.00 0.00 0.00 5.19
52 53 1.329256 TTCCCGAGAGCTATACAGGC 58.671 55.000 0.00 0.00 0.00 4.85
53 54 4.402056 TTTTTCCCGAGAGCTATACAGG 57.598 45.455 0.00 0.00 0.00 4.00
108 109 9.079833 CGCTGAAACATTTCTAATCATTTGAAT 57.920 29.630 5.97 0.00 38.02 2.57
116 119 6.467047 CACATGTCGCTGAAACATTTCTAATC 59.533 38.462 0.00 0.00 35.19 1.75
120 123 3.058016 CCACATGTCGCTGAAACATTTCT 60.058 43.478 0.00 0.00 35.19 2.52
133 136 2.979814 TCTATTGGACCCACATGTCG 57.020 50.000 0.00 0.00 36.07 4.35
134 137 3.136443 TGGATCTATTGGACCCACATGTC 59.864 47.826 0.00 0.00 34.42 3.06
138 141 1.843851 GGTGGATCTATTGGACCCACA 59.156 52.381 14.94 0.00 46.66 4.17
139 142 2.127708 AGGTGGATCTATTGGACCCAC 58.872 52.381 4.97 4.97 44.75 4.61
143 146 3.181461 CCTGACAGGTGGATCTATTGGAC 60.181 52.174 13.84 0.00 0.00 4.02
180 183 4.386951 TCGGCACCCCACATGTCG 62.387 66.667 0.00 0.00 46.37 4.35
198 201 2.603135 TACCGAGAGCTAAACCGCGC 62.603 60.000 0.00 0.00 34.40 6.86
199 202 0.179156 TTACCGAGAGCTAAACCGCG 60.179 55.000 0.00 0.00 34.40 6.46
200 203 1.925185 CTTTACCGAGAGCTAAACCGC 59.075 52.381 0.00 0.00 0.00 5.68
211 216 3.131396 ACTTGCAGTTGTCTTTACCGAG 58.869 45.455 0.00 0.00 0.00 4.63
213 218 2.869801 TGACTTGCAGTTGTCTTTACCG 59.130 45.455 14.55 0.00 34.57 4.02
254 259 1.207811 AGATGTCATGTCGCATGTCCA 59.792 47.619 16.01 14.23 0.00 4.02
259 264 2.353889 GCAAAGAGATGTCATGTCGCAT 59.646 45.455 4.43 0.00 0.00 4.73
260 265 1.733912 GCAAAGAGATGTCATGTCGCA 59.266 47.619 4.43 0.00 0.00 5.10
263 268 5.007430 CCACATAGCAAAGAGATGTCATGTC 59.993 44.000 1.68 1.68 31.44 3.06
269 274 5.366186 AGAGATCCACATAGCAAAGAGATGT 59.634 40.000 0.00 0.00 34.11 3.06
271 276 5.278907 CGAGAGATCCACATAGCAAAGAGAT 60.279 44.000 0.00 0.00 0.00 2.75
281 286 0.952280 GACGCCGAGAGATCCACATA 59.048 55.000 0.00 0.00 0.00 2.29
282 287 0.753479 AGACGCCGAGAGATCCACAT 60.753 55.000 0.00 0.00 0.00 3.21
286 291 1.064946 CACAGACGCCGAGAGATCC 59.935 63.158 0.00 0.00 0.00 3.36
288 293 3.069980 GCCACAGACGCCGAGAGAT 62.070 63.158 0.00 0.00 0.00 2.75
289 294 3.749064 GCCACAGACGCCGAGAGA 61.749 66.667 0.00 0.00 0.00 3.10
310 315 1.004440 GAAGAAGGCACAGTCGGCT 60.004 57.895 0.00 0.00 45.04 5.52
315 320 0.532862 CACGGTGAAGAAGGCACAGT 60.533 55.000 0.74 0.00 43.63 3.55
316 321 0.532862 ACACGGTGAAGAAGGCACAG 60.533 55.000 16.29 0.00 37.99 3.66
329 334 0.464036 TTCTGCACAGAAGACACGGT 59.536 50.000 8.99 0.00 42.06 4.83
332 337 5.673337 TGTTATTTCTGCACAGAAGACAC 57.327 39.130 12.51 10.67 46.80 3.67
342 347 4.615682 CGGCAACAAGATGTTATTTCTGCA 60.616 41.667 0.00 0.00 38.77 4.41
343 348 3.853671 CGGCAACAAGATGTTATTTCTGC 59.146 43.478 0.00 0.00 38.77 4.26
345 350 4.518970 ACACGGCAACAAGATGTTATTTCT 59.481 37.500 0.00 0.00 38.77 2.52
347 352 4.320935 GGACACGGCAACAAGATGTTATTT 60.321 41.667 0.00 0.00 38.77 1.40
348 353 3.190535 GGACACGGCAACAAGATGTTATT 59.809 43.478 0.00 0.00 38.77 1.40
349 354 2.747446 GGACACGGCAACAAGATGTTAT 59.253 45.455 0.00 0.00 38.77 1.89
350 355 2.147958 GGACACGGCAACAAGATGTTA 58.852 47.619 0.00 0.00 38.77 2.41
363 368 1.841663 CGGCAAAGACAAGGACACGG 61.842 60.000 0.00 0.00 0.00 4.94
384 389 8.110908 GGAGGGAGTATATGACAAGAGTAGTAT 58.889 40.741 0.00 0.00 0.00 2.12
387 392 5.413213 CGGAGGGAGTATATGACAAGAGTAG 59.587 48.000 0.00 0.00 0.00 2.57
394 399 2.490351 GGGACGGAGGGAGTATATGACA 60.490 54.545 0.00 0.00 0.00 3.58
410 415 6.304286 AAGTTGAGACACTTATTTCGGGACG 61.304 44.000 0.00 0.00 44.44 4.79
411 416 4.566987 AGTTGAGACACTTATTTCGGGAC 58.433 43.478 0.00 0.00 0.00 4.46
412 417 4.884668 AGTTGAGACACTTATTTCGGGA 57.115 40.909 0.00 0.00 0.00 5.14
413 418 5.238650 ACAAAGTTGAGACACTTATTTCGGG 59.761 40.000 0.00 0.00 35.87 5.14
414 419 6.300354 ACAAAGTTGAGACACTTATTTCGG 57.700 37.500 0.00 0.00 35.87 4.30
415 420 8.073355 AGTACAAAGTTGAGACACTTATTTCG 57.927 34.615 0.00 0.00 35.87 3.46
417 422 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
418 423 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
419 424 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
420 425 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
421 426 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
422 427 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
423 428 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
424 429 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
425 430 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
450 455 9.726438 AGTGTCTTGAGCTTAGTACAAATTTAT 57.274 29.630 0.00 0.00 0.00 1.40
451 456 9.555727 AAGTGTCTTGAGCTTAGTACAAATTTA 57.444 29.630 0.00 0.00 0.00 1.40
452 457 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
453 458 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
454 459 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
455 460 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
456 461 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
457 462 9.555727 AAAAATAAGTGTCTTGAGCTTAGTACA 57.444 29.630 0.00 0.00 0.00 2.90
458 463 9.813080 CAAAAATAAGTGTCTTGAGCTTAGTAC 57.187 33.333 0.00 0.00 0.00 2.73
459 464 8.999431 CCAAAAATAAGTGTCTTGAGCTTAGTA 58.001 33.333 0.00 0.00 0.00 1.82
460 465 7.719633 TCCAAAAATAAGTGTCTTGAGCTTAGT 59.280 33.333 0.00 0.00 0.00 2.24
461 466 8.017946 GTCCAAAAATAAGTGTCTTGAGCTTAG 58.982 37.037 0.00 0.00 0.00 2.18
462 467 7.307751 CGTCCAAAAATAAGTGTCTTGAGCTTA 60.308 37.037 0.00 0.00 0.00 3.09
463 468 6.513393 CGTCCAAAAATAAGTGTCTTGAGCTT 60.513 38.462 0.00 0.00 0.00 3.74
464 469 5.049405 CGTCCAAAAATAAGTGTCTTGAGCT 60.049 40.000 0.00 0.00 0.00 4.09
465 470 5.147162 CGTCCAAAAATAAGTGTCTTGAGC 58.853 41.667 0.00 0.00 0.00 4.26
466 471 5.468746 TCCGTCCAAAAATAAGTGTCTTGAG 59.531 40.000 0.00 0.00 0.00 3.02
467 472 5.369833 TCCGTCCAAAAATAAGTGTCTTGA 58.630 37.500 0.00 0.00 0.00 3.02
468 473 5.334879 CCTCCGTCCAAAAATAAGTGTCTTG 60.335 44.000 0.00 0.00 0.00 3.02
469 474 4.760204 CCTCCGTCCAAAAATAAGTGTCTT 59.240 41.667 0.00 0.00 0.00 3.01
470 475 4.324267 CCTCCGTCCAAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
471 476 3.439129 CCCTCCGTCCAAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
472 477 3.073356 TCCCTCCGTCCAAAAATAAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
473 478 3.681593 TCCCTCCGTCCAAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
474 479 3.329814 ACTCCCTCCGTCCAAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
475 480 3.951663 ACTCCCTCCGTCCAAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
476 481 5.703730 ATACTCCCTCCGTCCAAAAATAA 57.296 39.130 0.00 0.00 0.00 1.40
477 482 6.328148 ACATATACTCCCTCCGTCCAAAAATA 59.672 38.462 0.00 0.00 0.00 1.40
478 483 5.132144 ACATATACTCCCTCCGTCCAAAAAT 59.868 40.000 0.00 0.00 0.00 1.82
479 484 4.472108 ACATATACTCCCTCCGTCCAAAAA 59.528 41.667 0.00 0.00 0.00 1.94
480 485 4.035112 ACATATACTCCCTCCGTCCAAAA 58.965 43.478 0.00 0.00 0.00 2.44
481 486 3.649843 ACATATACTCCCTCCGTCCAAA 58.350 45.455 0.00 0.00 0.00 3.28
482 487 3.323774 ACATATACTCCCTCCGTCCAA 57.676 47.619 0.00 0.00 0.00 3.53
483 488 3.323774 AACATATACTCCCTCCGTCCA 57.676 47.619 0.00 0.00 0.00 4.02
484 489 3.802675 GCAAACATATACTCCCTCCGTCC 60.803 52.174 0.00 0.00 0.00 4.79
485 490 3.391049 GCAAACATATACTCCCTCCGTC 58.609 50.000 0.00 0.00 0.00 4.79
486 491 2.104281 GGCAAACATATACTCCCTCCGT 59.896 50.000 0.00 0.00 0.00 4.69
487 492 2.767505 GGCAAACATATACTCCCTCCG 58.232 52.381 0.00 0.00 0.00 4.63
488 493 2.367567 TCGGCAAACATATACTCCCTCC 59.632 50.000 0.00 0.00 0.00 4.30
489 494 3.069729 ACTCGGCAAACATATACTCCCTC 59.930 47.826 0.00 0.00 0.00 4.30
490 495 3.039011 ACTCGGCAAACATATACTCCCT 58.961 45.455 0.00 0.00 0.00 4.20
491 496 3.131396 CACTCGGCAAACATATACTCCC 58.869 50.000 0.00 0.00 0.00 4.30
492 497 2.544267 GCACTCGGCAAACATATACTCC 59.456 50.000 0.00 0.00 43.97 3.85
493 498 3.861569 GCACTCGGCAAACATATACTC 57.138 47.619 0.00 0.00 43.97 2.59
532 537 1.376037 CCGAGTGTTGGGCTCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
541 546 2.049802 ACCGTACGCCGAGTGTTG 60.050 61.111 10.49 0.00 39.56 3.33
546 551 1.060122 GAAATTTCACCGTACGCCGAG 59.940 52.381 10.49 0.00 39.56 4.63
555 560 5.236478 AGAACACACTACTGAAATTTCACCG 59.764 40.000 16.91 10.90 32.90 4.94
565 570 6.537301 CCTTAAACACAAGAACACACTACTGA 59.463 38.462 0.00 0.00 0.00 3.41
571 576 3.697542 ACCCCTTAAACACAAGAACACAC 59.302 43.478 0.00 0.00 0.00 3.82
572 577 3.970842 ACCCCTTAAACACAAGAACACA 58.029 40.909 0.00 0.00 0.00 3.72
574 579 5.376756 ACTACCCCTTAAACACAAGAACA 57.623 39.130 0.00 0.00 0.00 3.18
618 623 1.065928 CGACAGCCACCTACGATCC 59.934 63.158 0.00 0.00 0.00 3.36
643 648 1.466851 GGGGGCAGCCATTTGATAGC 61.467 60.000 15.19 0.00 0.00 2.97
663 668 3.461982 GTCAGCGCGTGTCGAGTG 61.462 66.667 8.43 0.00 41.67 3.51
730 777 3.409856 GCACGTGCGATGGCTAAT 58.590 55.556 26.77 0.00 40.82 1.73
794 841 1.104577 GGAAGGAAACACAACCGGCA 61.105 55.000 0.00 0.00 0.00 5.69
911 960 3.740141 CGGTGGAACTAACTGTGTGAAGT 60.740 47.826 0.00 0.00 36.74 3.01
923 972 2.357760 GCAACGGCGGTGGAACTA 60.358 61.111 27.92 0.00 36.74 2.24
933 982 3.959991 GAGTGGAGGGAGCAACGGC 62.960 68.421 0.00 0.00 41.61 5.68
934 983 2.266055 GAGTGGAGGGAGCAACGG 59.734 66.667 0.00 0.00 0.00 4.44
936 985 1.003233 GTGGAGTGGAGGGAGCAAC 60.003 63.158 0.00 0.00 0.00 4.17
937 986 2.224159 GGTGGAGTGGAGGGAGCAA 61.224 63.158 0.00 0.00 0.00 3.91
939 988 3.403558 GGGTGGAGTGGAGGGAGC 61.404 72.222 0.00 0.00 0.00 4.70
940 989 3.077556 CGGGTGGAGTGGAGGGAG 61.078 72.222 0.00 0.00 0.00 4.30
943 992 4.394712 GTGCGGGTGGAGTGGAGG 62.395 72.222 0.00 0.00 0.00 4.30
945 994 2.463589 GAATGTGCGGGTGGAGTGGA 62.464 60.000 0.00 0.00 0.00 4.02
974 1024 3.857854 GCTCGAGCGACGGACGTA 61.858 66.667 23.61 0.00 44.60 3.57
1166 1264 0.736325 GTACTGCGCCTCAACGTCAT 60.736 55.000 4.18 0.00 34.88 3.06
1208 1306 3.810896 GTTGTTGGATCGGCGGCC 61.811 66.667 9.54 9.54 0.00 6.13
1209 1307 3.039202 CTGTTGTTGGATCGGCGGC 62.039 63.158 7.21 0.00 0.00 6.53
1210 1308 3.039202 GCTGTTGTTGGATCGGCGG 62.039 63.158 7.21 0.00 0.00 6.13
1211 1309 1.851021 TTGCTGTTGTTGGATCGGCG 61.851 55.000 0.00 0.00 36.40 6.46
1224 1322 1.293498 CTCGTAGGGCAGTTGCTGT 59.707 57.895 3.88 0.00 41.70 4.40
1263 1361 3.208594 CTCCGGCATCAGAATTTCATCA 58.791 45.455 0.00 0.00 0.00 3.07
1306 1404 1.130561 GGCGTTCTGAACCTGCATAAC 59.869 52.381 17.92 2.25 0.00 1.89
1458 1556 2.650226 TATCCGACGGCCCATCCAGA 62.650 60.000 9.66 0.00 34.01 3.86
1608 1706 0.972983 ATGACTGGCCTAGCGTCTGT 60.973 55.000 3.32 0.00 0.00 3.41
1621 1719 0.458543 AAGTAGTGCGCCGATGACTG 60.459 55.000 4.18 0.00 0.00 3.51
1636 1734 2.389962 GGTATTGGACCGTGCAAGTA 57.610 50.000 11.36 2.13 38.87 2.24
4668 9861 5.880332 TGCTTACTACATTGGAACTTGATCC 59.120 40.000 0.00 0.00 40.10 3.36
4703 9896 2.355132 ACATGAGTACGATCGGTCAGAC 59.645 50.000 20.98 8.92 0.00 3.51


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

AutoCloner maintained by Alex Coulton.