Multiple sequence alignment - TraesCS1D01G292000

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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 TraesCS1D01G292000 chr1D 100.000 3817 0 0 1 3817 391278857 391275041 0.000000e+00 7049
1 TraesCS1D01G292000 chr1D 92.365 406 21 6 3268 3668 391256457 391256057 1.540000e-158 569
2 TraesCS1D01G292000 chr1A 96.047 1872 52 6 376 2228 494023630 494025498 0.000000e+00 3027
3 TraesCS1D01G292000 chr1A 93.603 891 41 11 2311 3195 494025497 494026377 0.000000e+00 1315
4 TraesCS1D01G292000 chr1A 90.217 368 30 5 3304 3668 494028082 494028446 3.450000e-130 475
5 TraesCS1D01G292000 chr1A 96.460 226 6 1 70 293 494023351 494023576 4.660000e-99 372
6 TraesCS1D01G292000 chr1B 95.114 1535 60 5 696 2230 531535018 531536537 0.000000e+00 2405
7 TraesCS1D01G292000 chr1B 91.199 909 37 17 2311 3194 531536531 531537421 0.000000e+00 1195
8 TraesCS1D01G292000 chr1B 90.437 847 44 17 2378 3197 531650019 531650855 0.000000e+00 1081
9 TraesCS1D01G292000 chr1B 88.225 552 46 9 3268 3817 531537426 531537960 3.210000e-180 641
10 TraesCS1D01G292000 chr1B 90.069 433 37 4 3374 3804 531650913 531651341 1.200000e-154 556
11 TraesCS1D01G292000 chr1B 87.248 447 45 8 3374 3817 531578745 531579182 2.050000e-137 499
12 TraesCS1D01G292000 chr1B 89.457 313 20 2 376 688 531534680 531534979 2.150000e-102 383
13 TraesCS1D01G292000 chr1B 88.739 222 15 4 70 288 531534399 531534613 2.920000e-66 263
14 TraesCS1D01G292000 chr1B 94.118 68 4 0 3268 3335 531578689 531578756 1.880000e-18 104
15 TraesCS1D01G292000 chr3D 79.680 1186 190 37 1001 2172 453985593 453984445 0.000000e+00 808
16 TraesCS1D01G292000 chr3D 79.750 800 148 12 1003 1792 1993202 1992407 5.530000e-158 568
17 TraesCS1D01G292000 chr3D 82.116 397 63 7 2363 2752 453984197 453983802 2.200000e-87 333
18 TraesCS1D01G292000 chr3B 82.404 807 124 15 1001 1795 596412713 596411913 0.000000e+00 688
19 TraesCS1D01G292000 chr3B 82.116 397 63 7 2363 2752 596411314 596410919 2.200000e-87 333
20 TraesCS1D01G292000 chr3A 82.010 806 127 15 1001 1794 595934499 595933700 0.000000e+00 669
21 TraesCS1D01G292000 chr3A 81.414 382 59 9 2380 2752 595933103 595932725 6.200000e-78 302
22 TraesCS1D01G292000 chr7A 80.754 769 128 17 1003 1758 465586 464825 1.980000e-162 582
23 TraesCS1D01G292000 chrUn 85.124 363 45 5 1000 1362 354266472 354266825 2.800000e-96 363
24 TraesCS1D01G292000 chrUn 88.400 250 29 0 1113 1362 247902080 247902329 6.200000e-78 302
25 TraesCS1D01G292000 chr2D 84.066 364 47 5 1001 1362 636085977 636085623 1.310000e-89 340
26 TraesCS1D01G292000 chr5B 81.949 277 43 6 2494 2764 610348525 610348800 1.070000e-55 228
27 TraesCS1D01G292000 chr5B 91.753 97 7 1 2216 2312 668903691 668903786 2.390000e-27 134
28 TraesCS1D01G292000 chr2A 79.447 253 29 10 1015 1267 761070864 761071093 1.420000e-34 158
29 TraesCS1D01G292000 chr5A 93.548 93 6 0 2220 2312 502684141 502684049 5.140000e-29 139
30 TraesCS1D01G292000 chr5A 88.889 108 8 4 2227 2332 574193417 574193312 3.090000e-26 130
31 TraesCS1D01G292000 chr4A 92.632 95 7 0 2220 2314 207366983 207366889 1.850000e-28 137
32 TraesCS1D01G292000 chr7B 90.291 103 9 1 2216 2318 330253580 330253479 2.390000e-27 134
33 TraesCS1D01G292000 chr2B 91.667 96 8 0 2227 2322 250267229 250267324 2.390000e-27 134
34 TraesCS1D01G292000 chr2B 91.753 97 7 1 2216 2312 646145923 646146018 2.390000e-27 134
35 TraesCS1D01G292000 chr4B 90.722 97 8 1 2216 2312 42350090 42350185 1.110000e-25 128
36 TraesCS1D01G292000 chr4B 90.722 97 8 1 2216 2312 44252002 44252097 1.110000e-25 128


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 TraesCS1D01G292000 chr1D 391275041 391278857 3816 True 7049.00 7049 100.00000 1 3817 1 chr1D.!!$R2 3816
1 TraesCS1D01G292000 chr1A 494023351 494028446 5095 False 1297.25 3027 94.08175 70 3668 4 chr1A.!!$F1 3598
2 TraesCS1D01G292000 chr1B 531534399 531537960 3561 False 977.40 2405 90.54680 70 3817 5 chr1B.!!$F1 3747
3 TraesCS1D01G292000 chr1B 531650019 531651341 1322 False 818.50 1081 90.25300 2378 3804 2 chr1B.!!$F3 1426
4 TraesCS1D01G292000 chr3D 453983802 453985593 1791 True 570.50 808 80.89800 1001 2752 2 chr3D.!!$R2 1751
5 TraesCS1D01G292000 chr3D 1992407 1993202 795 True 568.00 568 79.75000 1003 1792 1 chr3D.!!$R1 789
6 TraesCS1D01G292000 chr3B 596410919 596412713 1794 True 510.50 688 82.26000 1001 2752 2 chr3B.!!$R1 1751
7 TraesCS1D01G292000 chr3A 595932725 595934499 1774 True 485.50 669 81.71200 1001 2752 2 chr3A.!!$R1 1751
8 TraesCS1D01G292000 chr7A 464825 465586 761 True 582.00 582 80.75400 1003 1758 1 chr7A.!!$R1 755

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
354 373 0.107017 GTATGATGTGGCCCTGCAGT 60.107 55.0 13.81 0.00 0.0 4.40 F
355 374 0.181114 TATGATGTGGCCCTGCAGTC 59.819 55.0 13.81 3.71 0.0 3.51 F
1372 1441 0.317160 CAACACCGTCTGCTACCTCA 59.683 55.0 0.00 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 1949 0.390472 CTCCTCCTCCTTGACGTTGC 60.390 60.000 0.0 0.0 0.00 4.17 R
1918 1996 1.692042 CCTGACCTCCCTGCTCCAT 60.692 63.158 0.0 0.0 0.00 3.41 R
2960 3166 1.000717 GAGCTTCGCAGATCCTCTACC 60.001 57.143 0.0 0.0 35.04 3.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.652421 AACCGAATAAACCAAAAACCGT 57.348 36.364 0.00 0.00 0.00 4.83
23 24 5.764487 AACCGAATAAACCAAAAACCGTA 57.236 34.783 0.00 0.00 0.00 4.02
24 25 5.963176 ACCGAATAAACCAAAAACCGTAT 57.037 34.783 0.00 0.00 0.00 3.06
25 26 7.446001 AACCGAATAAACCAAAAACCGTATA 57.554 32.000 0.00 0.00 0.00 1.47
26 27 7.446001 ACCGAATAAACCAAAAACCGTATAA 57.554 32.000 0.00 0.00 0.00 0.98
27 28 7.880105 ACCGAATAAACCAAAAACCGTATAAA 58.120 30.769 0.00 0.00 0.00 1.40
28 29 7.807433 ACCGAATAAACCAAAAACCGTATAAAC 59.193 33.333 0.00 0.00 0.00 2.01
29 30 7.273164 CCGAATAAACCAAAAACCGTATAAACC 59.727 37.037 0.00 0.00 0.00 3.27
30 31 7.007277 CGAATAAACCAAAAACCGTATAAACCG 59.993 37.037 0.00 0.00 0.00 4.44
31 32 5.764487 AAACCAAAAACCGTATAAACCGA 57.236 34.783 0.00 0.00 0.00 4.69
32 33 5.764487 AACCAAAAACCGTATAAACCGAA 57.236 34.783 0.00 0.00 0.00 4.30
33 34 5.107109 ACCAAAAACCGTATAAACCGAAC 57.893 39.130 0.00 0.00 0.00 3.95
34 35 4.023279 ACCAAAAACCGTATAAACCGAACC 60.023 41.667 0.00 0.00 0.00 3.62
35 36 4.150343 CAAAAACCGTATAAACCGAACCG 58.850 43.478 0.00 0.00 0.00 4.44
36 37 3.311486 AAACCGTATAAACCGAACCGA 57.689 42.857 0.00 0.00 0.00 4.69
37 38 3.311486 AACCGTATAAACCGAACCGAA 57.689 42.857 0.00 0.00 0.00 4.30
38 39 3.525268 ACCGTATAAACCGAACCGAAT 57.475 42.857 0.00 0.00 0.00 3.34
39 40 3.447742 ACCGTATAAACCGAACCGAATC 58.552 45.455 0.00 0.00 0.00 2.52
40 41 3.119173 ACCGTATAAACCGAACCGAATCA 60.119 43.478 0.00 0.00 0.00 2.57
41 42 3.864583 CCGTATAAACCGAACCGAATCAA 59.135 43.478 0.00 0.00 0.00 2.57
42 43 4.329528 CCGTATAAACCGAACCGAATCAAA 59.670 41.667 0.00 0.00 0.00 2.69
43 44 5.250332 CGTATAAACCGAACCGAATCAAAC 58.750 41.667 0.00 0.00 0.00 2.93
44 45 4.690184 ATAAACCGAACCGAATCAAACC 57.310 40.909 0.00 0.00 0.00 3.27
45 46 1.241165 AACCGAACCGAATCAAACCC 58.759 50.000 0.00 0.00 0.00 4.11
46 47 0.108963 ACCGAACCGAATCAAACCCA 59.891 50.000 0.00 0.00 0.00 4.51
47 48 1.240256 CCGAACCGAATCAAACCCAA 58.760 50.000 0.00 0.00 0.00 4.12
48 49 1.609555 CCGAACCGAATCAAACCCAAA 59.390 47.619 0.00 0.00 0.00 3.28
49 50 2.034812 CCGAACCGAATCAAACCCAAAA 59.965 45.455 0.00 0.00 0.00 2.44
50 51 3.491104 CCGAACCGAATCAAACCCAAAAA 60.491 43.478 0.00 0.00 0.00 1.94
51 52 3.487942 CGAACCGAATCAAACCCAAAAAC 59.512 43.478 0.00 0.00 0.00 2.43
52 53 3.462483 ACCGAATCAAACCCAAAAACC 57.538 42.857 0.00 0.00 0.00 3.27
53 54 2.103432 ACCGAATCAAACCCAAAAACCC 59.897 45.455 0.00 0.00 0.00 4.11
54 55 2.399448 CGAATCAAACCCAAAAACCCG 58.601 47.619 0.00 0.00 0.00 5.28
55 56 2.034812 CGAATCAAACCCAAAAACCCGA 59.965 45.455 0.00 0.00 0.00 5.14
56 57 3.491104 CGAATCAAACCCAAAAACCCGAA 60.491 43.478 0.00 0.00 0.00 4.30
57 58 2.963548 TCAAACCCAAAAACCCGAAC 57.036 45.000 0.00 0.00 0.00 3.95
58 59 1.134560 TCAAACCCAAAAACCCGAACG 59.865 47.619 0.00 0.00 0.00 3.95
59 60 0.179105 AAACCCAAAAACCCGAACGC 60.179 50.000 0.00 0.00 0.00 4.84
60 61 1.321074 AACCCAAAAACCCGAACGCA 61.321 50.000 0.00 0.00 0.00 5.24
61 62 1.299544 CCCAAAAACCCGAACGCAC 60.300 57.895 0.00 0.00 0.00 5.34
62 63 1.655959 CCAAAAACCCGAACGCACG 60.656 57.895 0.00 0.00 0.00 5.34
63 64 2.025013 AAAAACCCGAACGCACGC 59.975 55.556 0.00 0.00 0.00 5.34
64 65 3.472736 AAAAACCCGAACGCACGCC 62.473 57.895 0.00 0.00 0.00 5.68
107 108 0.428618 GCGAGTGAAACGACACGTAC 59.571 55.000 0.00 0.00 45.86 3.67
173 175 3.633609 ATGTCCAGCACATGCGGCT 62.634 57.895 6.65 6.65 44.70 5.52
265 267 1.803555 CAATACATGCACACGTGTCCA 59.196 47.619 20.49 18.13 42.51 4.02
293 305 2.083526 ACCATTCGGATGCATCAGCAG 61.084 52.381 27.25 15.07 45.45 4.24
316 335 4.715130 TCTACAGGGCGGCCACCT 62.715 66.667 31.59 10.21 39.43 4.00
323 342 4.397832 GGCGGCCACCTCGGTTAA 62.398 66.667 15.62 0.00 36.97 2.01
325 344 2.435410 CGGCCACCTCGGTTAACC 60.435 66.667 15.13 15.13 36.97 2.85
340 359 5.272283 GGTTAACCCGATTCTCTGTATGA 57.728 43.478 14.16 0.00 0.00 2.15
341 360 5.855045 GGTTAACCCGATTCTCTGTATGAT 58.145 41.667 14.16 0.00 0.00 2.45
342 361 5.696724 GGTTAACCCGATTCTCTGTATGATG 59.303 44.000 14.16 0.00 0.00 3.07
343 362 6.281405 GTTAACCCGATTCTCTGTATGATGT 58.719 40.000 0.00 0.00 0.00 3.06
344 363 4.327982 ACCCGATTCTCTGTATGATGTG 57.672 45.455 0.00 0.00 0.00 3.21
345 364 3.070159 ACCCGATTCTCTGTATGATGTGG 59.930 47.826 0.00 0.00 0.00 4.17
346 365 3.062763 CCGATTCTCTGTATGATGTGGC 58.937 50.000 0.00 0.00 0.00 5.01
347 366 3.062763 CGATTCTCTGTATGATGTGGCC 58.937 50.000 0.00 0.00 0.00 5.36
348 367 3.406764 GATTCTCTGTATGATGTGGCCC 58.593 50.000 0.00 0.00 0.00 5.80
349 368 2.180946 TCTCTGTATGATGTGGCCCT 57.819 50.000 0.00 0.00 0.00 5.19
350 369 1.764723 TCTCTGTATGATGTGGCCCTG 59.235 52.381 0.00 0.00 0.00 4.45
351 370 0.181114 TCTGTATGATGTGGCCCTGC 59.819 55.000 0.00 0.00 0.00 4.85
352 371 0.107066 CTGTATGATGTGGCCCTGCA 60.107 55.000 0.00 0.00 0.00 4.41
353 372 0.107066 TGTATGATGTGGCCCTGCAG 60.107 55.000 6.78 6.78 0.00 4.41
354 373 0.107017 GTATGATGTGGCCCTGCAGT 60.107 55.000 13.81 0.00 0.00 4.40
355 374 0.181114 TATGATGTGGCCCTGCAGTC 59.819 55.000 13.81 3.71 0.00 3.51
356 375 1.855441 ATGATGTGGCCCTGCAGTCA 61.855 55.000 13.81 8.18 0.00 3.41
357 376 2.034687 ATGTGGCCCTGCAGTCAC 59.965 61.111 13.81 17.07 0.00 3.67
358 377 3.574074 ATGTGGCCCTGCAGTCACC 62.574 63.158 21.37 16.14 0.00 4.02
362 381 4.284550 GCCCTGCAGTCACCCCAA 62.285 66.667 13.81 0.00 0.00 4.12
363 382 2.034687 CCCTGCAGTCACCCCAAG 59.965 66.667 13.81 0.00 0.00 3.61
364 383 2.833913 CCCTGCAGTCACCCCAAGT 61.834 63.158 13.81 0.00 0.00 3.16
365 384 1.151450 CCTGCAGTCACCCCAAGTT 59.849 57.895 13.81 0.00 0.00 2.66
366 385 0.468029 CCTGCAGTCACCCCAAGTTT 60.468 55.000 13.81 0.00 0.00 2.66
367 386 1.402787 CTGCAGTCACCCCAAGTTTT 58.597 50.000 5.25 0.00 0.00 2.43
368 387 1.756538 CTGCAGTCACCCCAAGTTTTT 59.243 47.619 5.25 0.00 0.00 1.94
435 461 2.416431 CCCTGCTTAATTTGACAGCTGC 60.416 50.000 15.27 7.45 34.42 5.25
585 611 1.303561 TGCATGTGAGCCAGAACCC 60.304 57.895 0.00 0.00 0.00 4.11
708 774 2.004733 AGCATGTCATGTCATGTCACG 58.995 47.619 26.51 8.12 44.68 4.35
815 881 0.669932 GGCAGCGCTGATCTATCCTG 60.670 60.000 40.21 11.77 0.00 3.86
946 1012 1.935933 CATAAGTACCACGCCTCCAC 58.064 55.000 0.00 0.00 0.00 4.02
1033 1102 2.380365 TCAGTCCATTGGCTGAGCT 58.620 52.632 19.51 0.00 36.89 4.09
1098 1167 0.327591 ACTTCCCCGTCTACTCGTCT 59.672 55.000 0.00 0.00 0.00 4.18
1372 1441 0.317160 CAACACCGTCTGCTACCTCA 59.683 55.000 0.00 0.00 0.00 3.86
1874 1949 1.333636 AAGGAGATCGAGGTGGCCAG 61.334 60.000 5.11 0.00 0.00 4.85
1901 1979 0.556380 AAGGAGGAGGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
1907 1985 0.634465 GAGGAGGAGGAGGAGAAGGT 59.366 60.000 0.00 0.00 0.00 3.50
2162 2240 2.626743 ACTACTACACCGCAAAGTGAGT 59.373 45.455 5.60 7.03 40.34 3.41
2190 2268 1.824230 ACTCGCTCTGCTCTCTTCATT 59.176 47.619 0.00 0.00 0.00 2.57
2196 2274 3.260740 CTCTGCTCTCTTCATTGTCACC 58.739 50.000 0.00 0.00 0.00 4.02
2214 2292 5.645067 TGTCACCTTGAATAATCTTCAGCAG 59.355 40.000 0.00 0.00 0.00 4.24
2229 2307 8.854614 ATCTTCAGCAGTCTTTGTTTATTACT 57.145 30.769 0.00 0.00 0.00 2.24
2230 2308 8.311650 TCTTCAGCAGTCTTTGTTTATTACTC 57.688 34.615 0.00 0.00 0.00 2.59
2231 2309 7.387948 TCTTCAGCAGTCTTTGTTTATTACTCC 59.612 37.037 0.00 0.00 0.00 3.85
2232 2310 5.938125 TCAGCAGTCTTTGTTTATTACTCCC 59.062 40.000 0.00 0.00 0.00 4.30
2233 2311 5.940470 CAGCAGTCTTTGTTTATTACTCCCT 59.060 40.000 0.00 0.00 0.00 4.20
2234 2312 6.092807 CAGCAGTCTTTGTTTATTACTCCCTC 59.907 42.308 0.00 0.00 0.00 4.30
2235 2313 5.354513 GCAGTCTTTGTTTATTACTCCCTCC 59.645 44.000 0.00 0.00 0.00 4.30
2236 2314 5.880887 CAGTCTTTGTTTATTACTCCCTCCC 59.119 44.000 0.00 0.00 0.00 4.30
2237 2315 5.791141 AGTCTTTGTTTATTACTCCCTCCCT 59.209 40.000 0.00 0.00 0.00 4.20
2239 2317 6.598457 GTCTTTGTTTATTACTCCCTCCCTTC 59.402 42.308 0.00 0.00 0.00 3.46
2240 2318 5.446260 TTGTTTATTACTCCCTCCCTTCC 57.554 43.478 0.00 0.00 0.00 3.46
2241 2319 4.440808 TGTTTATTACTCCCTCCCTTCCA 58.559 43.478 0.00 0.00 0.00 3.53
2243 2321 5.313772 TGTTTATTACTCCCTCCCTTCCAAA 59.686 40.000 0.00 0.00 0.00 3.28
2244 2322 6.183361 TGTTTATTACTCCCTCCCTTCCAAAA 60.183 38.462 0.00 0.00 0.00 2.44
2245 2323 6.668133 TTATTACTCCCTCCCTTCCAAAAT 57.332 37.500 0.00 0.00 0.00 1.82
2247 2325 5.710409 TTACTCCCTCCCTTCCAAAATAG 57.290 43.478 0.00 0.00 0.00 1.73
2250 2328 4.166919 ACTCCCTCCCTTCCAAAATAGATG 59.833 45.833 0.00 0.00 0.00 2.90
2251 2329 4.379875 TCCCTCCCTTCCAAAATAGATGA 58.620 43.478 0.00 0.00 0.00 2.92
2252 2330 4.166144 TCCCTCCCTTCCAAAATAGATGAC 59.834 45.833 0.00 0.00 0.00 3.06
2254 2332 5.372373 CCTCCCTTCCAAAATAGATGACTC 58.628 45.833 0.00 0.00 0.00 3.36
2255 2333 5.104360 CCTCCCTTCCAAAATAGATGACTCA 60.104 44.000 0.00 0.00 0.00 3.41
2256 2334 6.387192 TCCCTTCCAAAATAGATGACTCAA 57.613 37.500 0.00 0.00 0.00 3.02
2258 2336 6.012508 TCCCTTCCAAAATAGATGACTCAACT 60.013 38.462 0.00 0.00 0.00 3.16
2260 2338 7.177392 CCCTTCCAAAATAGATGACTCAACTTT 59.823 37.037 0.00 0.00 0.00 2.66
2261 2339 8.025445 CCTTCCAAAATAGATGACTCAACTTTG 58.975 37.037 0.00 0.00 0.00 2.77
2262 2340 8.463930 TTCCAAAATAGATGACTCAACTTTGT 57.536 30.769 0.00 0.00 0.00 2.83
2264 2342 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2301 2379 9.719355 ACAAAATTGGGTTATCTAATTTGGAAC 57.281 29.630 8.17 0.00 35.05 3.62
2302 2380 9.161629 CAAAATTGGGTTATCTAATTTGGAACC 57.838 33.333 0.43 12.74 39.09 3.62
2303 2381 6.709018 ATTGGGTTATCTAATTTGGAACCG 57.291 37.500 13.92 0.00 40.43 4.44
2304 2382 5.438698 TGGGTTATCTAATTTGGAACCGA 57.561 39.130 13.92 9.98 40.43 4.69
2305 2383 5.433526 TGGGTTATCTAATTTGGAACCGAG 58.566 41.667 13.92 0.00 40.43 4.63
2306 2384 4.820173 GGGTTATCTAATTTGGAACCGAGG 59.180 45.833 13.92 0.00 40.43 4.63
2308 2386 5.397109 GGTTATCTAATTTGGAACCGAGGGA 60.397 44.000 8.17 0.00 30.94 4.20
2894 3100 8.567948 TGATGTAACATCTTCTTGTTTCTTTCC 58.432 33.333 0.00 0.00 40.25 3.13
2895 3101 7.272037 TGTAACATCTTCTTGTTTCTTTCCC 57.728 36.000 0.00 0.00 40.25 3.97
2896 3102 7.060421 TGTAACATCTTCTTGTTTCTTTCCCT 58.940 34.615 0.00 0.00 40.25 4.20
2951 3157 9.791838 GTTTTGTTTTGTTAGTTTTCTTGACTG 57.208 29.630 0.00 0.00 0.00 3.51
2960 3166 5.975410 AGTTTTCTTGACTGAACTTCTCG 57.025 39.130 0.00 0.00 0.00 4.04
3089 3311 5.163754 CCGGTGAATCTCTGTTAAAATGGAC 60.164 44.000 0.00 0.00 0.00 4.02
3092 3314 6.094186 GGTGAATCTCTGTTAAAATGGACCTC 59.906 42.308 0.00 0.00 0.00 3.85
3098 3320 6.672218 TCTCTGTTAAAATGGACCTCTGGATA 59.328 38.462 0.00 0.00 0.00 2.59
3099 3321 7.348274 TCTCTGTTAAAATGGACCTCTGGATAT 59.652 37.037 0.00 0.00 0.00 1.63
3101 3323 8.651389 TCTGTTAAAATGGACCTCTGGATATAG 58.349 37.037 0.00 0.00 0.00 1.31
3102 3324 8.331931 TGTTAAAATGGACCTCTGGATATAGT 57.668 34.615 0.00 0.00 0.00 2.12
3140 3362 4.517832 CGTGAATCATGATCATCCAACCAT 59.482 41.667 9.06 0.00 0.00 3.55
3154 3376 3.759618 TCCAACCATATTTCCAAACGTCC 59.240 43.478 0.00 0.00 0.00 4.79
3171 3393 1.002684 GTCCGAGTACATCTACCAGCG 60.003 57.143 0.00 0.00 0.00 5.18
3216 3438 7.045126 AGATACTCTAATACTCTGTTGTGGC 57.955 40.000 0.00 0.00 0.00 5.01
3217 3439 6.836527 AGATACTCTAATACTCTGTTGTGGCT 59.163 38.462 0.00 0.00 0.00 4.75
3218 3440 5.078411 ACTCTAATACTCTGTTGTGGCTG 57.922 43.478 0.00 0.00 0.00 4.85
3219 3441 4.772624 ACTCTAATACTCTGTTGTGGCTGA 59.227 41.667 0.00 0.00 0.00 4.26
3220 3442 5.246203 ACTCTAATACTCTGTTGTGGCTGAA 59.754 40.000 0.00 0.00 0.00 3.02
3221 3443 6.109156 TCTAATACTCTGTTGTGGCTGAAA 57.891 37.500 0.00 0.00 0.00 2.69
3222 3444 6.530120 TCTAATACTCTGTTGTGGCTGAAAA 58.470 36.000 0.00 0.00 0.00 2.29
3223 3445 7.168219 TCTAATACTCTGTTGTGGCTGAAAAT 58.832 34.615 0.00 0.00 0.00 1.82
3224 3446 8.318412 TCTAATACTCTGTTGTGGCTGAAAATA 58.682 33.333 0.00 0.00 0.00 1.40
3225 3447 6.992063 ATACTCTGTTGTGGCTGAAAATAG 57.008 37.500 0.00 0.00 0.00 1.73
3226 3448 4.718961 ACTCTGTTGTGGCTGAAAATAGT 58.281 39.130 0.00 0.00 0.00 2.12
3227 3449 5.865085 ACTCTGTTGTGGCTGAAAATAGTA 58.135 37.500 0.00 0.00 0.00 1.82
3228 3450 5.701290 ACTCTGTTGTGGCTGAAAATAGTAC 59.299 40.000 0.00 0.00 0.00 2.73
3229 3451 5.865085 TCTGTTGTGGCTGAAAATAGTACT 58.135 37.500 0.00 0.00 0.00 2.73
3230 3452 6.296026 TCTGTTGTGGCTGAAAATAGTACTT 58.704 36.000 0.00 0.00 0.00 2.24
3231 3453 6.770785 TCTGTTGTGGCTGAAAATAGTACTTT 59.229 34.615 0.00 0.00 0.00 2.66
3232 3454 6.966021 TGTTGTGGCTGAAAATAGTACTTTC 58.034 36.000 0.00 0.00 34.09 2.62
3233 3455 6.770785 TGTTGTGGCTGAAAATAGTACTTTCT 59.229 34.615 0.00 0.00 34.51 2.52
3234 3456 7.041372 TGTTGTGGCTGAAAATAGTACTTTCTC 60.041 37.037 0.00 0.00 34.51 2.87
3235 3457 6.769512 TGTGGCTGAAAATAGTACTTTCTCT 58.230 36.000 0.00 0.00 34.51 3.10
3236 3458 6.650807 TGTGGCTGAAAATAGTACTTTCTCTG 59.349 38.462 0.00 0.00 34.51 3.35
3237 3459 6.651225 GTGGCTGAAAATAGTACTTTCTCTGT 59.349 38.462 0.00 0.00 34.51 3.41
3238 3460 7.817962 GTGGCTGAAAATAGTACTTTCTCTGTA 59.182 37.037 0.00 0.00 34.51 2.74
3239 3461 8.540388 TGGCTGAAAATAGTACTTTCTCTGTAT 58.460 33.333 0.00 0.00 34.51 2.29
3253 3475 9.900710 ACTTTCTCTGTATACATTATAAGAGCG 57.099 33.333 5.91 3.73 32.32 5.03
3254 3476 9.900710 CTTTCTCTGTATACATTATAAGAGCGT 57.099 33.333 5.91 0.00 32.32 5.07
3273 3495 8.828688 AGAGCGTTTAGATTACTACTTTGTTT 57.171 30.769 0.00 0.00 0.00 2.83
3330 5217 4.023193 AGTCTTTATTTTGTCCTTGCACCG 60.023 41.667 0.00 0.00 0.00 4.94
3365 5252 3.526931 TTCTGAACTCGGCTAATGGAG 57.473 47.619 0.00 0.00 36.36 3.86
3379 5266 1.381599 TGGAGGATGCATTTGCCCC 60.382 57.895 0.00 0.00 41.18 5.80
3400 5287 5.290386 CCCTTGTAACGGAGATTCAGATAC 58.710 45.833 0.00 0.00 0.00 2.24
3406 5293 7.537715 TGTAACGGAGATTCAGATACGTAAAA 58.462 34.615 0.00 0.00 33.85 1.52
3429 5318 5.054477 ACGCCAACATGTATATCCTACAAC 58.946 41.667 0.00 0.00 0.00 3.32
3448 5337 5.312895 ACAACAGTAATACAGTTCCATGCA 58.687 37.500 0.00 0.00 0.00 3.96
3491 5380 5.471116 ACAAAAGTTTTACCCGGTCTATCAC 59.529 40.000 0.00 0.00 0.00 3.06
3566 5455 2.032924 GTGGTCCTTGAAAAAGACACCG 59.967 50.000 0.00 0.00 31.99 4.94
3571 5460 1.001378 CTTGAAAAAGACACCGCTGGG 60.001 52.381 0.00 0.00 40.11 4.45
3584 5473 1.361668 CGCTGGGGAAATGAGACGTG 61.362 60.000 0.00 0.00 0.00 4.49
3675 5567 3.948473 TGAAGACCGTTCCAACAATGAAA 59.052 39.130 0.00 0.00 0.00 2.69
3700 5592 6.992715 AGGTTACACATGAATAGGCATCTAAC 59.007 38.462 0.00 0.00 0.00 2.34
3725 5617 4.202245 TGGGTAGTTCTATGTTGACTGC 57.798 45.455 0.00 0.00 0.00 4.40
3741 5633 3.054728 TGACTGCGAGGAAAATTATCCCA 60.055 43.478 0.00 0.00 40.59 4.37
3742 5634 3.545703 ACTGCGAGGAAAATTATCCCAG 58.454 45.455 0.00 0.00 40.59 4.45
3747 5639 4.035675 GCGAGGAAAATTATCCCAGAACTG 59.964 45.833 0.00 0.00 40.59 3.16
3770 5662 6.216569 TGAAGTTACTGCTTTAGTCACAGAG 58.783 40.000 0.00 0.00 40.89 3.35
3789 5681 5.540337 ACAGAGAAGTTTGATCACACTCCTA 59.460 40.000 14.69 0.00 0.00 2.94
3808 5700 9.384764 CACTCCTATGTATATGAATACTCGAGA 57.615 37.037 21.68 2.92 39.05 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.008619 ACGGTTTTTGGTTTATTCGGTTT 57.991 34.783 0.00 0.00 0.00 3.27
1 2 4.652421 ACGGTTTTTGGTTTATTCGGTT 57.348 36.364 0.00 0.00 0.00 4.44
4 5 7.007277 CGGTTTATACGGTTTTTGGTTTATTCG 59.993 37.037 0.00 0.00 0.00 3.34
5 6 8.020244 TCGGTTTATACGGTTTTTGGTTTATTC 58.980 33.333 0.00 0.00 0.00 1.75
6 7 7.880105 TCGGTTTATACGGTTTTTGGTTTATT 58.120 30.769 0.00 0.00 0.00 1.40
7 8 7.446001 TCGGTTTATACGGTTTTTGGTTTAT 57.554 32.000 0.00 0.00 0.00 1.40
8 9 6.867662 TCGGTTTATACGGTTTTTGGTTTA 57.132 33.333 0.00 0.00 0.00 2.01
9 10 5.764487 TCGGTTTATACGGTTTTTGGTTT 57.236 34.783 0.00 0.00 0.00 3.27
10 11 5.507149 GGTTCGGTTTATACGGTTTTTGGTT 60.507 40.000 0.00 0.00 0.00 3.67
11 12 4.023279 GGTTCGGTTTATACGGTTTTTGGT 60.023 41.667 0.00 0.00 0.00 3.67
12 13 4.475028 GGTTCGGTTTATACGGTTTTTGG 58.525 43.478 0.00 0.00 0.00 3.28
13 14 4.084118 TCGGTTCGGTTTATACGGTTTTTG 60.084 41.667 0.00 0.00 0.00 2.44
14 15 4.061596 TCGGTTCGGTTTATACGGTTTTT 58.938 39.130 0.00 0.00 0.00 1.94
15 16 3.658709 TCGGTTCGGTTTATACGGTTTT 58.341 40.909 0.00 0.00 0.00 2.43
16 17 3.311486 TCGGTTCGGTTTATACGGTTT 57.689 42.857 0.00 0.00 0.00 3.27
17 18 3.311486 TTCGGTTCGGTTTATACGGTT 57.689 42.857 0.00 0.00 0.00 4.44
18 19 3.119173 TGATTCGGTTCGGTTTATACGGT 60.119 43.478 0.00 0.00 0.00 4.83
19 20 3.446799 TGATTCGGTTCGGTTTATACGG 58.553 45.455 0.00 0.00 0.00 4.02
20 21 5.250332 GTTTGATTCGGTTCGGTTTATACG 58.750 41.667 0.00 0.00 0.00 3.06
21 22 5.447683 GGGTTTGATTCGGTTCGGTTTATAC 60.448 44.000 0.00 0.00 0.00 1.47
22 23 4.635324 GGGTTTGATTCGGTTCGGTTTATA 59.365 41.667 0.00 0.00 0.00 0.98
23 24 3.441222 GGGTTTGATTCGGTTCGGTTTAT 59.559 43.478 0.00 0.00 0.00 1.40
24 25 2.813172 GGGTTTGATTCGGTTCGGTTTA 59.187 45.455 0.00 0.00 0.00 2.01
25 26 1.610038 GGGTTTGATTCGGTTCGGTTT 59.390 47.619 0.00 0.00 0.00 3.27
26 27 1.241165 GGGTTTGATTCGGTTCGGTT 58.759 50.000 0.00 0.00 0.00 4.44
27 28 0.108963 TGGGTTTGATTCGGTTCGGT 59.891 50.000 0.00 0.00 0.00 4.69
28 29 1.240256 TTGGGTTTGATTCGGTTCGG 58.760 50.000 0.00 0.00 0.00 4.30
29 30 3.357166 TTTTGGGTTTGATTCGGTTCG 57.643 42.857 0.00 0.00 0.00 3.95
30 31 3.805422 GGTTTTTGGGTTTGATTCGGTTC 59.195 43.478 0.00 0.00 0.00 3.62
31 32 3.432467 GGGTTTTTGGGTTTGATTCGGTT 60.432 43.478 0.00 0.00 0.00 4.44
32 33 2.103432 GGGTTTTTGGGTTTGATTCGGT 59.897 45.455 0.00 0.00 0.00 4.69
33 34 2.761559 GGGTTTTTGGGTTTGATTCGG 58.238 47.619 0.00 0.00 0.00 4.30
34 35 2.034812 TCGGGTTTTTGGGTTTGATTCG 59.965 45.455 0.00 0.00 0.00 3.34
35 36 3.737032 TCGGGTTTTTGGGTTTGATTC 57.263 42.857 0.00 0.00 0.00 2.52
36 37 3.738590 CGTTCGGGTTTTTGGGTTTGATT 60.739 43.478 0.00 0.00 0.00 2.57
37 38 2.223852 CGTTCGGGTTTTTGGGTTTGAT 60.224 45.455 0.00 0.00 0.00 2.57
38 39 1.134560 CGTTCGGGTTTTTGGGTTTGA 59.865 47.619 0.00 0.00 0.00 2.69
39 40 1.562017 CGTTCGGGTTTTTGGGTTTG 58.438 50.000 0.00 0.00 0.00 2.93
40 41 0.179105 GCGTTCGGGTTTTTGGGTTT 60.179 50.000 0.00 0.00 0.00 3.27
41 42 1.321074 TGCGTTCGGGTTTTTGGGTT 61.321 50.000 0.00 0.00 0.00 4.11
42 43 1.753463 TGCGTTCGGGTTTTTGGGT 60.753 52.632 0.00 0.00 0.00 4.51
43 44 1.299544 GTGCGTTCGGGTTTTTGGG 60.300 57.895 0.00 0.00 0.00 4.12
44 45 1.655959 CGTGCGTTCGGGTTTTTGG 60.656 57.895 0.00 0.00 0.00 3.28
45 46 2.290082 GCGTGCGTTCGGGTTTTTG 61.290 57.895 3.95 0.00 0.00 2.44
46 47 2.025013 GCGTGCGTTCGGGTTTTT 59.975 55.556 3.95 0.00 0.00 1.94
47 48 3.956317 GGCGTGCGTTCGGGTTTT 61.956 61.111 3.95 0.00 0.00 2.43
54 55 2.251642 AAAGTCAGGGCGTGCGTTC 61.252 57.895 1.51 0.00 0.00 3.95
55 56 2.203153 AAAGTCAGGGCGTGCGTT 60.203 55.556 1.51 0.17 0.00 4.84
56 57 2.933878 TTCAAAGTCAGGGCGTGCGT 62.934 55.000 1.51 0.00 0.00 5.24
57 58 2.175184 CTTCAAAGTCAGGGCGTGCG 62.175 60.000 1.51 0.00 0.00 5.34
58 59 1.166531 ACTTCAAAGTCAGGGCGTGC 61.167 55.000 1.51 0.00 32.86 5.34
59 60 0.588252 CACTTCAAAGTCAGGGCGTG 59.412 55.000 0.00 0.00 37.08 5.34
60 61 0.468226 TCACTTCAAAGTCAGGGCGT 59.532 50.000 0.00 0.00 37.08 5.68
61 62 1.151668 CTCACTTCAAAGTCAGGGCG 58.848 55.000 0.00 0.00 37.08 6.13
62 63 1.876156 CACTCACTTCAAAGTCAGGGC 59.124 52.381 0.00 0.00 37.08 5.19
63 64 3.134458 GTCACTCACTTCAAAGTCAGGG 58.866 50.000 0.00 0.00 37.08 4.45
64 65 2.797156 CGTCACTCACTTCAAAGTCAGG 59.203 50.000 0.00 0.00 37.08 3.86
65 66 2.797156 CCGTCACTCACTTCAAAGTCAG 59.203 50.000 0.00 0.00 37.08 3.51
66 67 2.429250 TCCGTCACTCACTTCAAAGTCA 59.571 45.455 0.00 0.00 37.08 3.41
67 68 3.053455 CTCCGTCACTCACTTCAAAGTC 58.947 50.000 0.00 0.00 37.08 3.01
68 69 2.803492 GCTCCGTCACTCACTTCAAAGT 60.803 50.000 0.00 0.00 40.60 2.66
107 108 3.252215 TGGGTTAAACTTGTCAGCAATCG 59.748 43.478 0.00 0.00 33.65 3.34
169 171 2.455032 CAGACAAGAAGACGATAGCCG 58.545 52.381 0.00 0.00 45.44 5.52
173 175 4.783764 TTCTGCAGACAAGAAGACGATA 57.216 40.909 18.03 0.00 0.00 2.92
288 292 0.106335 CCCTGTAGATGCCTCTGCTG 59.894 60.000 8.42 7.63 38.71 4.41
293 305 2.423446 CCGCCCTGTAGATGCCTC 59.577 66.667 0.00 0.00 0.00 4.70
319 338 6.201044 CACATCATACAGAGAATCGGGTTAAC 59.799 42.308 0.00 0.00 42.67 2.01
322 341 4.443457 CCACATCATACAGAGAATCGGGTT 60.443 45.833 0.00 0.00 42.67 4.11
323 342 3.070159 CCACATCATACAGAGAATCGGGT 59.930 47.826 0.00 0.00 42.67 5.28
325 344 3.062763 GCCACATCATACAGAGAATCGG 58.937 50.000 0.00 0.00 42.67 4.18
327 346 3.072184 AGGGCCACATCATACAGAGAATC 59.928 47.826 6.18 0.00 0.00 2.52
329 348 2.171237 CAGGGCCACATCATACAGAGAA 59.829 50.000 6.18 0.00 0.00 2.87
330 349 1.764723 CAGGGCCACATCATACAGAGA 59.235 52.381 6.18 0.00 0.00 3.10
332 351 0.181114 GCAGGGCCACATCATACAGA 59.819 55.000 6.18 0.00 0.00 3.41
333 352 0.107066 TGCAGGGCCACATCATACAG 60.107 55.000 6.18 0.00 0.00 2.74
334 353 0.107066 CTGCAGGGCCACATCATACA 60.107 55.000 6.18 0.00 0.00 2.29
335 354 0.107017 ACTGCAGGGCCACATCATAC 60.107 55.000 19.93 0.00 0.00 2.39
337 356 1.077212 GACTGCAGGGCCACATCAT 60.077 57.895 19.93 0.00 0.00 2.45
338 357 2.352422 GACTGCAGGGCCACATCA 59.648 61.111 19.93 0.00 0.00 3.07
339 358 2.042831 GTGACTGCAGGGCCACATC 61.043 63.158 19.93 4.92 0.00 3.06
340 359 2.034687 GTGACTGCAGGGCCACAT 59.965 61.111 19.93 0.00 0.00 3.21
341 360 4.269523 GGTGACTGCAGGGCCACA 62.270 66.667 26.23 13.91 0.00 4.17
345 364 4.284550 TTGGGGTGACTGCAGGGC 62.285 66.667 19.93 10.32 0.00 5.19
346 365 2.034687 CTTGGGGTGACTGCAGGG 59.965 66.667 19.93 0.00 0.00 4.45
347 366 0.468029 AAACTTGGGGTGACTGCAGG 60.468 55.000 19.93 0.00 0.00 4.85
348 367 1.402787 AAAACTTGGGGTGACTGCAG 58.597 50.000 13.48 13.48 0.00 4.41
349 368 1.859302 AAAAACTTGGGGTGACTGCA 58.141 45.000 0.00 0.00 0.00 4.41
367 386 6.361768 AAAACTTGGGGTGACTTGTAAAAA 57.638 33.333 0.00 0.00 0.00 1.94
368 387 6.166982 CAAAAACTTGGGGTGACTTGTAAAA 58.833 36.000 0.00 0.00 0.00 1.52
369 388 5.725362 CAAAAACTTGGGGTGACTTGTAAA 58.275 37.500 0.00 0.00 0.00 2.01
370 389 4.382147 GCAAAAACTTGGGGTGACTTGTAA 60.382 41.667 0.00 0.00 0.00 2.41
371 390 3.131400 GCAAAAACTTGGGGTGACTTGTA 59.869 43.478 0.00 0.00 0.00 2.41
372 391 2.093711 GCAAAAACTTGGGGTGACTTGT 60.094 45.455 0.00 0.00 0.00 3.16
373 392 2.549926 GCAAAAACTTGGGGTGACTTG 58.450 47.619 0.00 0.00 0.00 3.16
374 393 1.484653 GGCAAAAACTTGGGGTGACTT 59.515 47.619 0.00 0.00 0.00 3.01
435 461 3.980134 CAGAGAGTAGCAATGCATCGTAG 59.020 47.826 8.35 0.00 0.00 3.51
750 816 5.387788 TCCAATTGATGTCTCCATTATGGG 58.612 41.667 11.76 2.50 38.32 4.00
1017 1086 0.323178 CCAAGCTCAGCCAATGGACT 60.323 55.000 2.05 0.00 31.72 3.85
1033 1102 2.429930 CCAGACGCTTCCCACCAA 59.570 61.111 0.00 0.00 0.00 3.67
1098 1167 0.318441 CCTTGACCGTCTTGAGCTCA 59.682 55.000 13.74 13.74 0.00 4.26
1372 1441 2.042162 AGGGGAAGTTGTTGATGCAGAT 59.958 45.455 0.00 0.00 0.00 2.90
1683 1758 1.305381 CTCCTTGGACGAGACCCCT 60.305 63.158 0.00 0.00 0.00 4.79
1874 1949 0.390472 CTCCTCCTCCTTGACGTTGC 60.390 60.000 0.00 0.00 0.00 4.17
1918 1996 1.692042 CCTGACCTCCCTGCTCCAT 60.692 63.158 0.00 0.00 0.00 3.41
2162 2240 2.640302 GCAGAGCGAGTGAGGTGGA 61.640 63.158 0.00 0.00 0.00 4.02
2190 2268 5.559770 TGCTGAAGATTATTCAAGGTGACA 58.440 37.500 0.00 0.00 0.00 3.58
2196 2274 7.814642 ACAAAGACTGCTGAAGATTATTCAAG 58.185 34.615 0.00 0.00 0.00 3.02
2214 2292 6.063496 AGGGAGGGAGTAATAAACAAAGAC 57.937 41.667 0.00 0.00 0.00 3.01
2226 2304 4.967871 TCTATTTTGGAAGGGAGGGAGTA 58.032 43.478 0.00 0.00 0.00 2.59
2227 2305 3.815507 TCTATTTTGGAAGGGAGGGAGT 58.184 45.455 0.00 0.00 0.00 3.85
2228 2306 4.413520 TCATCTATTTTGGAAGGGAGGGAG 59.586 45.833 0.00 0.00 0.00 4.30
2229 2307 4.166144 GTCATCTATTTTGGAAGGGAGGGA 59.834 45.833 0.00 0.00 0.00 4.20
2230 2308 4.166919 AGTCATCTATTTTGGAAGGGAGGG 59.833 45.833 0.00 0.00 0.00 4.30
2231 2309 5.104360 TGAGTCATCTATTTTGGAAGGGAGG 60.104 44.000 0.00 0.00 0.00 4.30
2232 2310 5.994250 TGAGTCATCTATTTTGGAAGGGAG 58.006 41.667 0.00 0.00 0.00 4.30
2233 2311 6.012508 AGTTGAGTCATCTATTTTGGAAGGGA 60.013 38.462 1.70 0.00 0.00 4.20
2234 2312 6.183347 AGTTGAGTCATCTATTTTGGAAGGG 58.817 40.000 1.70 0.00 0.00 3.95
2235 2313 7.693969 AAGTTGAGTCATCTATTTTGGAAGG 57.306 36.000 4.14 0.00 0.00 3.46
2236 2314 8.571336 ACAAAGTTGAGTCATCTATTTTGGAAG 58.429 33.333 14.35 0.00 40.00 3.46
2237 2315 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2239 2317 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2278 2356 7.397761 TCGGTTCCAAATTAGATAACCCAATTT 59.602 33.333 0.00 0.00 36.98 1.82
2279 2357 6.893005 TCGGTTCCAAATTAGATAACCCAATT 59.107 34.615 0.00 0.00 36.98 2.32
2280 2358 6.428295 TCGGTTCCAAATTAGATAACCCAAT 58.572 36.000 0.00 0.00 36.98 3.16
2282 2360 5.433526 CTCGGTTCCAAATTAGATAACCCA 58.566 41.667 0.00 0.00 36.98 4.51
2283 2361 4.820173 CCTCGGTTCCAAATTAGATAACCC 59.180 45.833 0.00 0.00 36.98 4.11
2284 2362 4.820173 CCCTCGGTTCCAAATTAGATAACC 59.180 45.833 0.00 0.00 36.95 2.85
2286 2364 5.427481 ACTCCCTCGGTTCCAAATTAGATAA 59.573 40.000 0.00 0.00 0.00 1.75
2287 2365 4.966805 ACTCCCTCGGTTCCAAATTAGATA 59.033 41.667 0.00 0.00 0.00 1.98
2288 2366 3.780850 ACTCCCTCGGTTCCAAATTAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2292 2370 4.586306 AATACTCCCTCGGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
2293 2371 4.720273 AGTAATACTCCCTCGGTTCCAAAT 59.280 41.667 0.00 0.00 0.00 2.32
2294 2372 4.081309 CAGTAATACTCCCTCGGTTCCAAA 60.081 45.833 0.00 0.00 0.00 3.28
2296 2374 3.028850 CAGTAATACTCCCTCGGTTCCA 58.971 50.000 0.00 0.00 0.00 3.53
2297 2375 3.029570 ACAGTAATACTCCCTCGGTTCC 58.970 50.000 0.00 0.00 0.00 3.62
2298 2376 4.886489 AGTACAGTAATACTCCCTCGGTTC 59.114 45.833 0.00 0.00 28.86 3.62
2299 2377 4.864726 AGTACAGTAATACTCCCTCGGTT 58.135 43.478 0.00 0.00 28.86 4.44
2300 2378 4.516652 AGTACAGTAATACTCCCTCGGT 57.483 45.455 0.00 0.00 28.86 4.69
2301 2379 4.037684 CCAAGTACAGTAATACTCCCTCGG 59.962 50.000 0.00 0.00 34.18 4.63
2302 2380 4.643784 ACCAAGTACAGTAATACTCCCTCG 59.356 45.833 0.00 0.00 34.18 4.63
2303 2381 6.832900 ACTACCAAGTACAGTAATACTCCCTC 59.167 42.308 0.00 0.00 34.18 4.30
2304 2382 6.739664 ACTACCAAGTACAGTAATACTCCCT 58.260 40.000 0.00 0.00 34.18 4.20
2341 2419 7.014134 TCCTGCTCATGTCAAAACATCTTTTAA 59.986 33.333 0.00 0.00 44.41 1.52
2343 2421 5.302568 TCCTGCTCATGTCAAAACATCTTTT 59.697 36.000 0.00 0.00 44.41 2.27
2358 2436 1.743321 GAGTAGCCGCTCCTGCTCAT 61.743 60.000 0.00 0.00 42.11 2.90
2951 3157 3.243267 GCAGATCCTCTACCGAGAAGTTC 60.243 52.174 0.00 0.00 39.74 3.01
2960 3166 1.000717 GAGCTTCGCAGATCCTCTACC 60.001 57.143 0.00 0.00 35.04 3.18
3051 3272 3.907894 TCACCGGCAACTTTATTCAAC 57.092 42.857 0.00 0.00 0.00 3.18
3125 3347 7.470424 CGTTTGGAAATATGGTTGGATGATCAT 60.470 37.037 8.25 8.25 0.00 2.45
3127 3349 6.183360 ACGTTTGGAAATATGGTTGGATGATC 60.183 38.462 0.00 0.00 0.00 2.92
3128 3350 5.656416 ACGTTTGGAAATATGGTTGGATGAT 59.344 36.000 0.00 0.00 0.00 2.45
3129 3351 5.013547 ACGTTTGGAAATATGGTTGGATGA 58.986 37.500 0.00 0.00 0.00 2.92
3130 3352 5.323371 ACGTTTGGAAATATGGTTGGATG 57.677 39.130 0.00 0.00 0.00 3.51
3140 3362 4.517952 TGTACTCGGACGTTTGGAAATA 57.482 40.909 0.00 0.00 0.00 1.40
3154 3376 1.941294 ACTCGCTGGTAGATGTACTCG 59.059 52.381 0.00 2.48 0.00 4.18
3197 3419 5.330455 TCAGCCACAACAGAGTATTAGAG 57.670 43.478 0.00 0.00 0.00 2.43
3198 3420 5.738619 TTCAGCCACAACAGAGTATTAGA 57.261 39.130 0.00 0.00 0.00 2.10
3199 3421 6.801539 TTTTCAGCCACAACAGAGTATTAG 57.198 37.500 0.00 0.00 0.00 1.73
3200 3422 8.100791 ACTATTTTCAGCCACAACAGAGTATTA 58.899 33.333 0.00 0.00 0.00 0.98
3201 3423 6.942576 ACTATTTTCAGCCACAACAGAGTATT 59.057 34.615 0.00 0.00 0.00 1.89
3202 3424 6.476378 ACTATTTTCAGCCACAACAGAGTAT 58.524 36.000 0.00 0.00 0.00 2.12
3203 3425 5.865085 ACTATTTTCAGCCACAACAGAGTA 58.135 37.500 0.00 0.00 0.00 2.59
3204 3426 4.718961 ACTATTTTCAGCCACAACAGAGT 58.281 39.130 0.00 0.00 0.00 3.24
3205 3427 5.934625 AGTACTATTTTCAGCCACAACAGAG 59.065 40.000 0.00 0.00 0.00 3.35
3206 3428 5.865085 AGTACTATTTTCAGCCACAACAGA 58.135 37.500 0.00 0.00 0.00 3.41
3207 3429 6.560253 AAGTACTATTTTCAGCCACAACAG 57.440 37.500 0.00 0.00 0.00 3.16
3208 3430 6.770785 AGAAAGTACTATTTTCAGCCACAACA 59.229 34.615 8.19 0.00 37.08 3.33
3209 3431 7.173390 AGAGAAAGTACTATTTTCAGCCACAAC 59.827 37.037 8.19 0.00 37.08 3.32
3210 3432 7.173218 CAGAGAAAGTACTATTTTCAGCCACAA 59.827 37.037 8.19 0.00 37.08 3.33
3211 3433 6.650807 CAGAGAAAGTACTATTTTCAGCCACA 59.349 38.462 8.19 0.00 37.08 4.17
3212 3434 6.651225 ACAGAGAAAGTACTATTTTCAGCCAC 59.349 38.462 8.19 0.00 37.08 5.01
3213 3435 6.769512 ACAGAGAAAGTACTATTTTCAGCCA 58.230 36.000 8.19 0.00 37.08 4.75
3214 3436 8.950208 ATACAGAGAAAGTACTATTTTCAGCC 57.050 34.615 8.19 0.00 37.08 4.85
3227 3449 9.900710 CGCTCTTATAATGTATACAGAGAAAGT 57.099 33.333 17.28 0.00 33.08 2.66
3228 3450 9.900710 ACGCTCTTATAATGTATACAGAGAAAG 57.099 33.333 17.28 14.34 33.08 2.62
3246 3468 9.918630 AACAAAGTAGTAATCTAAACGCTCTTA 57.081 29.630 0.00 0.00 0.00 2.10
3247 3469 8.828688 AACAAAGTAGTAATCTAAACGCTCTT 57.171 30.769 0.00 0.00 0.00 2.85
3248 3470 8.709646 CAAACAAAGTAGTAATCTAAACGCTCT 58.290 33.333 0.00 0.00 0.00 4.09
3249 3471 7.477733 GCAAACAAAGTAGTAATCTAAACGCTC 59.522 37.037 0.00 0.00 0.00 5.03
3250 3472 7.295930 GCAAACAAAGTAGTAATCTAAACGCT 58.704 34.615 0.00 0.00 0.00 5.07
3251 3473 6.522165 GGCAAACAAAGTAGTAATCTAAACGC 59.478 38.462 0.00 0.00 0.00 4.84
3252 3474 7.744715 CAGGCAAACAAAGTAGTAATCTAAACG 59.255 37.037 0.00 0.00 0.00 3.60
3253 3475 8.565416 ACAGGCAAACAAAGTAGTAATCTAAAC 58.435 33.333 0.00 0.00 0.00 2.01
3254 3476 8.685838 ACAGGCAAACAAAGTAGTAATCTAAA 57.314 30.769 0.00 0.00 0.00 1.85
3255 3477 8.685838 AACAGGCAAACAAAGTAGTAATCTAA 57.314 30.769 0.00 0.00 0.00 2.10
3256 3478 8.685838 AAACAGGCAAACAAAGTAGTAATCTA 57.314 30.769 0.00 0.00 0.00 1.98
3257 3479 7.519970 CGAAACAGGCAAACAAAGTAGTAATCT 60.520 37.037 0.00 0.00 0.00 2.40
3258 3480 6.577427 CGAAACAGGCAAACAAAGTAGTAATC 59.423 38.462 0.00 0.00 0.00 1.75
3259 3481 6.261381 TCGAAACAGGCAAACAAAGTAGTAAT 59.739 34.615 0.00 0.00 0.00 1.89
3260 3482 5.585445 TCGAAACAGGCAAACAAAGTAGTAA 59.415 36.000 0.00 0.00 0.00 2.24
3261 3483 5.117584 TCGAAACAGGCAAACAAAGTAGTA 58.882 37.500 0.00 0.00 0.00 1.82
3262 3484 3.942748 TCGAAACAGGCAAACAAAGTAGT 59.057 39.130 0.00 0.00 0.00 2.73
3263 3485 4.545823 TCGAAACAGGCAAACAAAGTAG 57.454 40.909 0.00 0.00 0.00 2.57
3264 3486 6.811253 ATATCGAAACAGGCAAACAAAGTA 57.189 33.333 0.00 0.00 0.00 2.24
3265 3487 5.705609 ATATCGAAACAGGCAAACAAAGT 57.294 34.783 0.00 0.00 0.00 2.66
3266 3488 6.027749 GGTATATCGAAACAGGCAAACAAAG 58.972 40.000 0.00 0.00 0.00 2.77
3273 3495 4.196193 CCTTTGGTATATCGAAACAGGCA 58.804 43.478 0.00 0.00 0.00 4.75
3365 5252 1.484038 TACAAGGGGCAAATGCATCC 58.516 50.000 0.00 8.15 44.36 3.51
3379 5266 5.579718 ACGTATCTGAATCTCCGTTACAAG 58.420 41.667 0.00 0.00 0.00 3.16
3400 5287 5.235616 AGGATATACATGTTGGCGTTTTACG 59.764 40.000 2.30 0.00 45.88 3.18
3406 5293 4.948341 TGTAGGATATACATGTTGGCGT 57.052 40.909 2.30 0.00 0.00 5.68
3429 5318 5.585844 TGATGTGCATGGAACTGTATTACTG 59.414 40.000 0.00 0.00 0.00 2.74
3448 5337 1.660607 GTGTTGATCGCGACATGATGT 59.339 47.619 12.93 0.00 40.41 3.06
3491 5380 4.582656 AGCCACAGCAGAGTATTAGAGTAG 59.417 45.833 0.00 0.00 43.56 2.57
3566 5455 0.036388 TCACGTCTCATTTCCCCAGC 60.036 55.000 0.00 0.00 0.00 4.85
3571 5460 1.550976 ACCCTCTCACGTCTCATTTCC 59.449 52.381 0.00 0.00 0.00 3.13
3584 5473 2.574399 GTCGCACTCCACCCTCTC 59.426 66.667 0.00 0.00 0.00 3.20
3675 5567 5.636903 AGATGCCTATTCATGTGTAACCT 57.363 39.130 0.00 0.00 34.36 3.50
3700 5592 6.480320 GCAGTCAACATAGAACTACCCATTAG 59.520 42.308 0.00 0.00 0.00 1.73
3725 5617 5.428253 TCAGTTCTGGGATAATTTTCCTCG 58.572 41.667 13.76 6.35 35.97 4.63
3741 5633 6.702282 GTGACTAAAGCAGTAACTTCAGTTCT 59.298 38.462 0.00 0.00 37.72 3.01
3742 5634 6.479001 TGTGACTAAAGCAGTAACTTCAGTTC 59.521 38.462 0.00 0.00 39.21 3.01
3747 5639 6.448006 TCTCTGTGACTAAAGCAGTAACTTC 58.552 40.000 0.00 0.00 39.21 3.01
3770 5662 9.988815 ATATACATAGGAGTGTGATCAAACTTC 57.011 33.333 19.67 17.71 33.62 3.01
3789 5681 7.123397 AGGCACATCTCGAGTATTCATATACAT 59.877 37.037 13.13 0.00 39.30 2.29


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

AutoCloner maintained by Alex Coulton.